From fbacf78beedac0008a0a2083960fbb775ab007bc Mon Sep 17 00:00:00 2001 From: gleisonm Date: Tue, 14 Apr 2026 15:55:10 -0300 Subject: [PATCH 01/13] add nf-core tests samples --- assets/test_samplesheet.csv | 2 ++ conf/test.config | 13 +++++++------ 2 files changed, 9 insertions(+), 6 deletions(-) create mode 100644 assets/test_samplesheet.csv diff --git a/assets/test_samplesheet.csv b/assets/test_samplesheet.csv new file mode 100644 index 0000000..a419495 --- /dev/null +++ b/assets/test_samplesheet.csv @@ -0,0 +1,2 @@ +sample,gtf +TEST_SAMPLE,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf diff --git a/conf/test.config b/conf/test.config index 1f92698..21b8def 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,12 +20,13 @@ params { max_time = '6.h' // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = "${projectDir}/assets/samplesheet.csv" - reference_genome = "${projectDir}/assets/R64-1-1.fasta" - reference_gtf = "${projectDir}/assets/R64-1-1.transcripts.gtf" + input = "${projectDir}/assets/test_samplesheet.csv" // Genome references - genome = 'R64-1-1' + reference_genome = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + reference_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf" + reference_gff = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3" + + // Functional annotation + pfam_db = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/test_starfusion_dfam.hmm" } From ec96b5913b1186b43423fc8e49861d7ec536e323 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 16:04:15 -0300 Subject: [PATCH 02/13] fix gtf test input --- assets/test_samplesheet.csv | 2 +- assets/test_stringtie_output.gtf | 18 ++++++++++++++++++ conf/test.config | 10 +++++++++- workflows/nottocode.nf | 19 ++++++++++++++++--- 4 files changed, 44 insertions(+), 5 deletions(-) create mode 100644 assets/test_stringtie_output.gtf diff --git a/assets/test_samplesheet.csv b/assets/test_samplesheet.csv index a419495..fba9059 100644 --- a/assets/test_samplesheet.csv +++ b/assets/test_samplesheet.csv @@ -1,2 +1,2 @@ sample,gtf -TEST_SAMPLE,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf +TEST_SAMPLE,assets/test_stringtie_output.gtf diff --git a/assets/test_stringtie_output.gtf b/assets/test_stringtie_output.gtf new file mode 100644 index 0000000..6d67e61 --- /dev/null +++ b/assets/test_stringtie_output.gtf @@ -0,0 +1,18 @@ +# StringTie version 2.2.1 - simulated output for sarscov2 genome (MT192765.1) +# Test data compatible with nf-core/test-datasets sarscov2 genome +# All transcripts have TPM >= 1.5 to pass StringTie merge -T 1 threshold +MT192765.1 StringTie transcript 259 21548 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; cov "100.000000"; FPKM "50.000000"; TPM "5.000000"; +MT192765.1 StringTie exon 259 13461 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; cov "100.000000"; +MT192765.1 StringTie exon 13461 21545 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "2"; cov "100.000000"; +MT192765.1 StringTie transcript 21556 25377 1000 + . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; cov "80.000000"; FPKM "40.000000"; TPM "4.000000"; +MT192765.1 StringTie exon 21556 25374 1000 + . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; cov "80.000000"; +MT192765.1 StringTie transcript 25386 26213 500 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; cov "50.000000"; FPKM "25.000000"; TPM "2.500000"; +MT192765.1 StringTie exon 25386 26210 500 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; cov "50.000000"; +MT192765.1 StringTie transcript 26238 26465 200 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; cov "20.000000"; FPKM "10.000000"; TPM "2.000000"; +MT192765.1 StringTie exon 26238 26462 200 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1"; cov "20.000000"; +MT192765.1 StringTie transcript 26516 27184 300 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; cov "30.000000"; FPKM "15.000000"; TPM "1.500000"; +MT192765.1 StringTie exon 26516 27181 300 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; cov "30.000000"; +MT192765.1 StringTie transcript 27195 27380 150 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; cov "15.000000"; FPKM "7.500000"; TPM "1.750000"; +MT192765.1 StringTie exon 27195 27377 150 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; cov "15.000000"; +MT192765.1 StringTie transcript 28267 29526 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; cov "40.000000"; FPKM "20.000000"; TPM "2.000000"; +MT192765.1 StringTie exon 28267 29523 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; cov "40.000000"; diff --git a/conf/test.config b/conf/test.config index 21b8def..9055bd8 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,13 +20,21 @@ params { max_time = '6.h' // Input data + // test_samplesheet.csv aponta para GTF sintético no formato StringTie (com linhas transcript + TPM) + // O path é expandido dinamicamente no test.config via Nextflow antes do split input = "${projectDir}/assets/test_samplesheet.csv" + test_gtf = "${projectDir}/assets/test_stringtie_output.gtf" - // Genome references + // Genome references (sarscov2 - compatível com o GTF de teste) reference_genome = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" reference_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf" reference_gff = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3" // Functional annotation pfam_db = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/test_starfusion_dfam.hmm" + + // Desabilitar filtro TPM nos testes (GTF de teste já contém transcritos com TPM acima do limiar) + // ou manter habilitado com threshold baixo para validar o módulo de filtragem + filter_by_tpm = true + tpm_threshold = 0.1 } diff --git a/workflows/nottocode.nf b/workflows/nottocode.nf index ac9f27b..4b5eac2 100644 --- a/workflows/nottocode.nf +++ b/workflows/nottocode.nf @@ -93,9 +93,22 @@ workflow NOTTOCODE { meta.id = row.sample meta.single_end = true - def gtf_file = file(row.gtf) - if (!gtf_file.exists()) { - error("ERROR: Arquivo GTF não encontrado: ${row.gtf}") + // Resolve GTF path: absolute, URL, or relative to projectDir + def gtf_path = row.gtf.trim() + def gtf_file + if (gtf_path.startsWith('http://') || gtf_path.startsWith('https://') || gtf_path.startsWith('s3://')) { + gtf_file = file(gtf_path) + } else if (gtf_path.startsWith('/')) { + gtf_file = file(gtf_path) + if (!gtf_file.exists()) { + error("ERROR: Arquivo GTF não encontrado: ${gtf_path}") + } + } else { + // Path relativo: resolver relativo ao projectDir + gtf_file = file("${projectDir}/${gtf_path}") + if (!gtf_file.exists()) { + error("ERROR: Arquivo GTF não encontrado: ${projectDir}/${gtf_path}") + } } return [meta, gtf_file] From efcbb7541fb3c7dc464874cdc37237b5a3483cd2 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 16:54:14 -0300 Subject: [PATCH 03/13] fix gtf test input --- assets/test_stringtie_output.gtf | 6 ++++++ modules/local/compare_transcriptomes/main.nf | 19 +++++++++++++++++-- 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/assets/test_stringtie_output.gtf b/assets/test_stringtie_output.gtf index 6d67e61..9e68b58 100644 --- a/assets/test_stringtie_output.gtf +++ b/assets/test_stringtie_output.gtf @@ -1,6 +1,8 @@ # StringTie version 2.2.1 - simulated output for sarscov2 genome (MT192765.1) # Test data compatible with nf-core/test-datasets sarscov2 genome # All transcripts have TPM >= 1.5 to pass StringTie merge -T 1 threshold +# MSTRG.1-7: regions overlapping known genes (will get class_code '=' or similar) +# MSTRG.8-9: novel intergenic regions (will get class_code 'u' - novel, not overlapping known genes) MT192765.1 StringTie transcript 259 21548 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; cov "100.000000"; FPKM "50.000000"; TPM "5.000000"; MT192765.1 StringTie exon 259 13461 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; cov "100.000000"; MT192765.1 StringTie exon 13461 21545 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "2"; cov "100.000000"; @@ -16,3 +18,7 @@ MT192765.1 StringTie transcript 27195 27380 150 + . gene_id "MSTRG.6"; transcrip MT192765.1 StringTie exon 27195 27377 150 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; cov "15.000000"; MT192765.1 StringTie transcript 28267 29526 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; cov "40.000000"; FPKM "20.000000"; TPM "2.000000"; MT192765.1 StringTie exon 28267 29523 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; cov "40.000000"; +MT192765.1 StringTie transcript 100 200 300 + . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; cov "30.000000"; FPKM "15.000000"; TPM "3.000000"; +MT192765.1 StringTie exon 100 200 300 + . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; cov "30.000000"; +MT192765.1 StringTie transcript 21550 21555 200 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; cov "20.000000"; FPKM "10.000000"; TPM "2.000000"; +MT192765.1 StringTie exon 21550 21555 200 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; cov "20.000000"; diff --git a/modules/local/compare_transcriptomes/main.nf b/modules/local/compare_transcriptomes/main.nf index 37287a3..1c286aa 100644 --- a/modules/local/compare_transcriptomes/main.nf +++ b/modules/local/compare_transcriptomes/main.nf @@ -81,7 +81,7 @@ process COMPARE_TRANSCRIPTOMES { cat("Verificação da diferença:", actual_diff == expected_diff, "\\n") # Filtrar GTF removendo proteínas codificantes - cat("Filtrando GTF para remover proteínas codificantes...\\n") + cat("Filtrando GTF para remover proteínas codificantes\\n") gtf_remove_prot <- dup_reference_annot %>% filter(transcript_id %in% classes_different) %>% filter(strand %in% c("+", "-")) @@ -98,7 +98,22 @@ process COMPARE_TRANSCRIPTOMES { output_file <- "${prefix}.remove_prot.gtf" cat("Exportando GTF filtrado para:", output_file, "\\n") - rtracklayer::export(gtf_remove_prot, output_file, format = "gtf") + if (nrow(gtf_remove_prot) == 0) { + cat("AVISO: Nenhum transcrito novel encontrado (todos são class_code '=').\\n") + cat("Criando arquivo GTF vazio de saída.\\n") + file.create(output_file) + } else { + # Converter data.frame para GRanges antes de exportar + gtf_granges <- GenomicRanges::makeGRangesFromDataFrame( + gtf_remove_prot, + keep.extra.columns = TRUE, + seqnames.field = "seqnames", + start.field = "start", + end.field = "end", + strand.field = "strand" + ) + rtracklayer::export(gtf_granges, output_file, format = "gtf") + } cat("Análise concluída com sucesso!\\n") sink() From 88ffefa3c103fdd62da608ed6b15823536941593 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 18:13:13 -0300 Subject: [PATCH 04/13] fix fasta test input --- modules/local/transdecoder/main.nf | 110 ++++++++++++++++------------- 1 file changed, 61 insertions(+), 49 deletions(-) diff --git a/modules/local/transdecoder/main.nf b/modules/local/transdecoder/main.nf index fd77e60..f1dcbc0 100644 --- a/modules/local/transdecoder/main.nf +++ b/modules/local/transdecoder/main.nf @@ -37,60 +37,72 @@ process TRANSDECODER_LONGORFS { echo "Data/hora de início: \$(date)" >> ${prefix}.log # Contar número de sequências no arquivo FASTA - seq_count=\$(grep -c "^>" ${fasta_file}) + # Usar || true para evitar exit 1 quando grep não encontra matches (arquivo vazio) + seq_count=\$(grep -c "^>" ${fasta_file} || true) + seq_count=\${seq_count:-0} echo "Número de sequências a serem analisadas: \$seq_count" >> ${prefix}.log - # Executar TransDecoder.LongOrfs - echo "Executando TransDecoder.LongOrfs..." >> ${prefix}.log - TransDecoder.LongOrfs \\ - -t ${fasta_file} \\ - --output_dir ${output_dir} \\ - ${args} \\ - 2>&1 | tee -a ${prefix}.log - - # Verificar se os arquivos de saída foram criados - if [ -d "${output_dir}" ]; then - echo "TransDecoder.LongOrfs concluído com sucesso" >> ${prefix}.log - - # Contar ORFs identificadas - if [ -f "${output_dir}/longest_orfs.pep" ]; then - orf_count=\$(grep -c "^>" ${output_dir}/longest_orfs.pep) - echo "Número de ORFs longas identificadas: \$orf_count" >> ${prefix}.log - fi - - # Listar arquivos criados - echo "Arquivos criados no diretório TransDecoder:" >> ${prefix}.log - ls -la ${output_dir}/ >> ${prefix}.log + # Verificar se o arquivo FASTA tem sequências + if [ "\$seq_count" -eq 0 ]; then + echo "AVISO: Arquivo FASTA vazio ou sem sequências. Criando outputs vazios." >> ${prefix}.log + mkdir -p ${output_dir} + touch ${output_dir}/longest_orfs.pep + touch ${output_dir}/longest_orfs.gff3 + touch ${output_dir}/longest_orfs.cds + echo "Análise ignorada (FASTA vazio)" >> ${prefix}.log + else + # Executar TransDecoder.LongOrfs + echo "Executando TransDecoder.LongOrfs..." >> ${prefix}.log + TransDecoder.LongOrfs \\ + -t ${fasta_file} \\ + --output_dir ${output_dir} \\ + ${args} \\ + 2>&1 | tee -a ${prefix}.log - # Estatísticas dos comprimentos das ORFs - if [ -f "${output_dir}/longest_orfs.pep" ]; then - echo "Estatísticas dos comprimentos das ORFs:" >> ${prefix}.log - grep -v "^>" ${output_dir}/longest_orfs.pep | awk '{print length(\$0)}' | sort -n | awk ' - BEGIN { sum = 0; count = 0; } - { - lengths[count] = \$1; - sum += \$1; - count++; - } - END { - if (count > 0) { - mean = sum / count; - if (count % 2 == 1) { - median = lengths[int(count/2)]; - } else { - median = (lengths[count/2-1] + lengths[count/2]) / 2; - } - print " Comprimento médio: " mean " aa"; - print " Comprimento mediano: " median " aa"; - print " Comprimento mínimo: " lengths[0] " aa"; - print " Comprimento máximo: " lengths[count-1] " aa"; + # Verificar se os arquivos de saída foram criados + if [ -d "${output_dir}" ]; then + echo "TransDecoder.LongOrfs concluído com sucesso" >> ${prefix}.log + + # Contar ORFs identificadas + if [ -f "${output_dir}/longest_orfs.pep" ]; then + orf_count=\$(grep -c "^>" ${output_dir}/longest_orfs.pep || true) + orf_count=\${orf_count:-0} + echo "Número de ORFs longas identificadas: \$orf_count" >> ${prefix}.log + fi + + # Listar arquivos criados + echo "Arquivos criados no diretório TransDecoder:" >> ${prefix}.log + ls -la ${output_dir}/ >> ${prefix}.log + + # Estatísticas dos comprimentos das ORFs + if [ -f "${output_dir}/longest_orfs.pep" ] && [ "\$orf_count" -gt 0 ]; then + echo "Estatísticas dos comprimentos das ORFs:" >> ${prefix}.log + grep -v "^>" ${output_dir}/longest_orfs.pep | awk '{print length(\$0)}' | sort -n | awk ' + BEGIN { sum = 0; count = 0; } + { + lengths[count] = \$1; + sum += \$1; + count++; } - }' >> ${prefix}.log + END { + if (count > 0) { + mean = sum / count; + if (count % 2 == 1) { + median = lengths[int(count/2)]; + } else { + median = (lengths[count/2-1] + lengths[count/2]) / 2; + } + print " Comprimento médio: " mean " aa"; + print " Comprimento mediano: " median " aa"; + print " Comprimento mínimo: " lengths[0] " aa"; + print " Comprimento máximo: " lengths[count-1] " aa"; + } + }' >> ${prefix}.log + fi + else + echo "ERRO: Diretório de saída não foi criado" >> ${prefix}.log + exit 1 fi - - else - echo "ERRO: Diretório de saída não foi criado" >> ${prefix}.log - exit 1 fi echo "Data/hora de término: \$(date)" >> ${prefix}.log From 1846da2421b929bdf5182b1fb7a34cec6ce221fe Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 18:41:43 -0300 Subject: [PATCH 05/13] fix test data input --- assets/test_stringtie_output.gtf | 62 +++++++++------- conf/test.config | 18 ++--- modules/local/transdecoder/main.nf | 110 +++++++++++++---------------- 3 files changed, 97 insertions(+), 93 deletions(-) diff --git a/assets/test_stringtie_output.gtf b/assets/test_stringtie_output.gtf index 9e68b58..1f56ca4 100644 --- a/assets/test_stringtie_output.gtf +++ b/assets/test_stringtie_output.gtf @@ -1,24 +1,38 @@ -# StringTie version 2.2.1 - simulated output for sarscov2 genome (MT192765.1) -# Test data compatible with nf-core/test-datasets sarscov2 genome -# All transcripts have TPM >= 1.5 to pass StringTie merge -T 1 threshold -# MSTRG.1-7: regions overlapping known genes (will get class_code '=' or similar) -# MSTRG.8-9: novel intergenic regions (will get class_code 'u' - novel, not overlapping known genes) -MT192765.1 StringTie transcript 259 21548 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; cov "100.000000"; FPKM "50.000000"; TPM "5.000000"; -MT192765.1 StringTie exon 259 13461 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; cov "100.000000"; -MT192765.1 StringTie exon 13461 21545 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "2"; cov "100.000000"; -MT192765.1 StringTie transcript 21556 25377 1000 + . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; cov "80.000000"; FPKM "40.000000"; TPM "4.000000"; -MT192765.1 StringTie exon 21556 25374 1000 + . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; cov "80.000000"; -MT192765.1 StringTie transcript 25386 26213 500 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; cov "50.000000"; FPKM "25.000000"; TPM "2.500000"; -MT192765.1 StringTie exon 25386 26210 500 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; cov "50.000000"; -MT192765.1 StringTie transcript 26238 26465 200 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; cov "20.000000"; FPKM "10.000000"; TPM "2.000000"; -MT192765.1 StringTie exon 26238 26462 200 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1"; cov "20.000000"; -MT192765.1 StringTie transcript 26516 27184 300 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; cov "30.000000"; FPKM "15.000000"; TPM "1.500000"; -MT192765.1 StringTie exon 26516 27181 300 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; cov "30.000000"; -MT192765.1 StringTie transcript 27195 27380 150 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; cov "15.000000"; FPKM "7.500000"; TPM "1.750000"; -MT192765.1 StringTie exon 27195 27377 150 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; cov "15.000000"; -MT192765.1 StringTie transcript 28267 29526 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; cov "40.000000"; FPKM "20.000000"; TPM "2.000000"; -MT192765.1 StringTie exon 28267 29523 400 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; cov "40.000000"; -MT192765.1 StringTie transcript 100 200 300 + . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; cov "30.000000"; FPKM "15.000000"; TPM "3.000000"; -MT192765.1 StringTie exon 100 200 300 + . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; cov "30.000000"; -MT192765.1 StringTie transcript 21550 21555 200 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; cov "20.000000"; FPKM "10.000000"; TPM "2.000000"; -MT192765.1 StringTie exon 21550 21555 200 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; cov "20.000000"; +# StringTie version 2.2.1 - simulated output for homo_sapiens chr22 test genome (40000 bp) +# Reference: nf-core/test-datasets modules homo_sapiens genome.fasta (chr22:1-40000) +# +# Gene structure in the test genome (chr22:1-40000, relative coords): +# ENSG00000233995 (pseudogene): 1-2611 +# ENSG00000239435 (pseudogene): 3337-10681 +# -- intergenic region --: 10682-18724 <-- novel transcripts placed here +# ENSG00000198445 (protein_coding): 18725-20784 +# ENSG00000287285 (lncRNA): 20869-28084 +# ENSG00000240122 (pseudogene): 23063-23459 +# ENSG00000283633 (lncRNA): 29885-40000 +# +# MSTRG.1.1 and MSTRG.2.1: novel intergenic transcripts (class_code 'u' in gffcompare) +# - multi-exon, total exon length > 600 nt -> sufficient for TransDecoder (min 100aa = 300nt) +# - all sequences exist in the hr22 genome FASTA so gffread can extract them +# MSTRG.3.1: partially overlaps ENSG00000239435 with different boundaries (class_code 'j' or 'o') +# - this tests the non-'=' class code path in COMPARE_TRANSCRIPTOMES +# +# All transcripts have TPM >= 1.5 to pass: +# 1. GTF_FILTER_TPM (threshold 0.1) +# 2. STRINGTIE_MERGE (-T 1) +# +chr22 StringTie transcript 11000 12800 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; cov "120.000000"; FPKM "60.000000"; TPM "6.000000"; +chr22 StringTie exon 11000 11320 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; cov "120.000000"; +chr22 StringTie exon 11600 12000 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "2"; cov "120.000000"; +chr22 StringTie exon 12200 12800 1000 + . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "3"; cov "120.000000"; +chr22 StringTie transcript 13500 15600 800 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; cov "80.000000"; FPKM "40.000000"; TPM "4.000000"; +chr22 StringTie exon 13500 14000 800 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; cov "80.000000"; +chr22 StringTie exon 14400 14900 800 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "2"; cov "80.000000"; +chr22 StringTie exon 15200 15600 800 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "3"; cov "80.000000"; +chr22 StringTie transcript 16000 17800 600 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; cov "60.000000"; FPKM "30.000000"; TPM "3.000000"; +chr22 StringTie exon 16000 16500 600 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; cov "60.000000"; +chr22 StringTie exon 16900 17400 600 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "2"; cov "60.000000"; +chr22 StringTie exon 17600 17800 600 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "3"; cov "60.000000"; +chr22 StringTie transcript 8000 10400 500 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; cov "50.000000"; FPKM "25.000000"; TPM "2.500000"; +chr22 StringTie exon 8000 8500 500 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1"; cov "50.000000"; +chr22 StringTie exon 9000 10000 500 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "2"; cov "50.000000"; +chr22 StringTie exon 10100 10400 500 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "3"; cov "50.000000"; diff --git a/conf/test.config b/conf/test.config index 9055bd8..5379067 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,20 +21,22 @@ params { // Input data // test_samplesheet.csv aponta para GTF sintético no formato StringTie (com linhas transcript + TPM) - // O path é expandido dinamicamente no test.config via Nextflow antes do split + // Transcritos em região intergênica chr22:10682-18724 (8042 bp) - suficiente para TransDecoder/CPC2/PLEK input = "${projectDir}/assets/test_samplesheet.csv" - test_gtf = "${projectDir}/assets/test_stringtie_output.gtf" - // Genome references (sarscov2 - compatível com o GTF de teste) - reference_genome = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" - reference_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf" - reference_gff = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3" + // Genome references: homo_sapiens chr22 test fragment (40000 bp) + // Usando o mesmo GTF como reference_gff pois o genome.gff3 do nf-core usa coordenadas + // absolutas do chr22 real (~16M bp) incompatíveis com o FASTA de teste (1-40000 bp) + reference_genome = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" + reference_gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + reference_gff = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" // Functional annotation pfam_db = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/test_starfusion_dfam.hmm" - // Desabilitar filtro TPM nos testes (GTF de teste já contém transcritos com TPM acima do limiar) - // ou manter habilitado com threshold baixo para validar o módulo de filtragem + // TPM filtering: manter habilitado com threshold baixo para testar o módulo GTF_FILTER_TPM + // Todos os transcritos de teste têm TPM >= 2.5 (passa pelo filtro 0.1 e pelo merge -T 1) filter_by_tpm = true tpm_threshold = 0.1 + } diff --git a/modules/local/transdecoder/main.nf b/modules/local/transdecoder/main.nf index f1dcbc0..fd77e60 100644 --- a/modules/local/transdecoder/main.nf +++ b/modules/local/transdecoder/main.nf @@ -37,72 +37,60 @@ process TRANSDECODER_LONGORFS { echo "Data/hora de início: \$(date)" >> ${prefix}.log # Contar número de sequências no arquivo FASTA - # Usar || true para evitar exit 1 quando grep não encontra matches (arquivo vazio) - seq_count=\$(grep -c "^>" ${fasta_file} || true) - seq_count=\${seq_count:-0} + seq_count=\$(grep -c "^>" ${fasta_file}) echo "Número de sequências a serem analisadas: \$seq_count" >> ${prefix}.log - # Verificar se o arquivo FASTA tem sequências - if [ "\$seq_count" -eq 0 ]; then - echo "AVISO: Arquivo FASTA vazio ou sem sequências. Criando outputs vazios." >> ${prefix}.log - mkdir -p ${output_dir} - touch ${output_dir}/longest_orfs.pep - touch ${output_dir}/longest_orfs.gff3 - touch ${output_dir}/longest_orfs.cds - echo "Análise ignorada (FASTA vazio)" >> ${prefix}.log - else - # Executar TransDecoder.LongOrfs - echo "Executando TransDecoder.LongOrfs..." >> ${prefix}.log - TransDecoder.LongOrfs \\ - -t ${fasta_file} \\ - --output_dir ${output_dir} \\ - ${args} \\ - 2>&1 | tee -a ${prefix}.log + # Executar TransDecoder.LongOrfs + echo "Executando TransDecoder.LongOrfs..." >> ${prefix}.log + TransDecoder.LongOrfs \\ + -t ${fasta_file} \\ + --output_dir ${output_dir} \\ + ${args} \\ + 2>&1 | tee -a ${prefix}.log + + # Verificar se os arquivos de saída foram criados + if [ -d "${output_dir}" ]; then + echo "TransDecoder.LongOrfs concluído com sucesso" >> ${prefix}.log - # Verificar se os arquivos de saída foram criados - if [ -d "${output_dir}" ]; then - echo "TransDecoder.LongOrfs concluído com sucesso" >> ${prefix}.log - - # Contar ORFs identificadas - if [ -f "${output_dir}/longest_orfs.pep" ]; then - orf_count=\$(grep -c "^>" ${output_dir}/longest_orfs.pep || true) - orf_count=\${orf_count:-0} - echo "Número de ORFs longas identificadas: \$orf_count" >> ${prefix}.log - fi - - # Listar arquivos criados - echo "Arquivos criados no diretório TransDecoder:" >> ${prefix}.log - ls -la ${output_dir}/ >> ${prefix}.log - - # Estatísticas dos comprimentos das ORFs - if [ -f "${output_dir}/longest_orfs.pep" ] && [ "\$orf_count" -gt 0 ]; then - echo "Estatísticas dos comprimentos das ORFs:" >> ${prefix}.log - grep -v "^>" ${output_dir}/longest_orfs.pep | awk '{print length(\$0)}' | sort -n | awk ' - BEGIN { sum = 0; count = 0; } - { - lengths[count] = \$1; - sum += \$1; - count++; - } - END { - if (count > 0) { - mean = sum / count; - if (count % 2 == 1) { - median = lengths[int(count/2)]; - } else { - median = (lengths[count/2-1] + lengths[count/2]) / 2; - } - print " Comprimento médio: " mean " aa"; - print " Comprimento mediano: " median " aa"; - print " Comprimento mínimo: " lengths[0] " aa"; - print " Comprimento máximo: " lengths[count-1] " aa"; + # Contar ORFs identificadas + if [ -f "${output_dir}/longest_orfs.pep" ]; then + orf_count=\$(grep -c "^>" ${output_dir}/longest_orfs.pep) + echo "Número de ORFs longas identificadas: \$orf_count" >> ${prefix}.log + fi + + # Listar arquivos criados + echo "Arquivos criados no diretório TransDecoder:" >> ${prefix}.log + ls -la ${output_dir}/ >> ${prefix}.log + + # Estatísticas dos comprimentos das ORFs + if [ -f "${output_dir}/longest_orfs.pep" ]; then + echo "Estatísticas dos comprimentos das ORFs:" >> ${prefix}.log + grep -v "^>" ${output_dir}/longest_orfs.pep | awk '{print length(\$0)}' | sort -n | awk ' + BEGIN { sum = 0; count = 0; } + { + lengths[count] = \$1; + sum += \$1; + count++; + } + END { + if (count > 0) { + mean = sum / count; + if (count % 2 == 1) { + median = lengths[int(count/2)]; + } else { + median = (lengths[count/2-1] + lengths[count/2]) / 2; } - }' >> ${prefix}.log - fi - else - echo "ERRO: Diretório de saída não foi criado" >> ${prefix}.log - exit 1 + print " Comprimento médio: " mean " aa"; + print " Comprimento mediano: " median " aa"; + print " Comprimento mínimo: " lengths[0] " aa"; + print " Comprimento máximo: " lengths[count-1] " aa"; + } + }' >> ${prefix}.log fi + + else + echo "ERRO: Diretório de saída não foi criado" >> ${prefix}.log + exit 1 fi echo "Data/hora de término: \$(date)" >> ${prefix}.log From 38a97e749bcf3495adfa0b46c6999b42c592ea73 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 19:21:19 -0300 Subject: [PATCH 06/13] fix test data input --- assets/generate_test_hmm.py | 84 ++++++++++++++++++++++++++ assets/test_protein.hmm | 117 ++++++++++++++++++++++++++++++++++++ conf/test.config | 5 +- 3 files changed, 205 insertions(+), 1 deletion(-) create mode 100644 assets/generate_test_hmm.py create mode 100644 assets/test_protein.hmm diff --git a/assets/generate_test_hmm.py b/assets/generate_test_hmm.py new file mode 100644 index 0000000..5652035 --- /dev/null +++ b/assets/generate_test_hmm.py @@ -0,0 +1,84 @@ +#!/usr/bin/env python3 +""" +Script para gerar um HMM proteico válido para testes do pipeline not2code. +Requer hmmbuild (pacote HMMER) instalado no ambiente. + +Uso: + micromamba activate nextflow + python3 assets/generate_test_hmm.py + +Ou diretamente com singularity: + singularity exec \ + /home/gmdazevedo/scratch/singularity_images/depot.galaxyproject.org-singularity-hmmer-3.4--hdbdd923_1.img \ + hmmbuild --amino assets/test_protein.hmm /dev/stdin << 'EOF' +# STOCKHOLM 1.0 +seq1 MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL +// +EOF +""" + +import subprocess +import sys +import os +import textwrap + +# Sequência proteica de teste (Globina humana - proteína bem caracterizada) +# Suficientemente longa para TransDecoder e para hmmbuild criar um HMM válido +TEST_SEQUENCE = """\ +MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD +NLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH +""".replace('\n', '') + +STOCKHOLM_CONTENT = f"""# STOCKHOLM 1.0 +#=GF ID test_protein_hmm +#=GF AC TEST0001.1 +#=GF DE Test protein HMM for not2code pipeline - amino acid profile +test_seq {TEST_SEQUENCE} +// +""" + +def main(): + # Caminho para o arquivo de saída + script_dir = os.path.dirname(os.path.abspath(__file__)) + output_hmm = os.path.join(script_dir, "test_protein.hmm") + sto_file = os.path.join(script_dir, "test_protein.sto") + + print(f"Gerando HMM proteico de teste em: {output_hmm}") + + # Escrever o alinhamento Stockholm + with open(sto_file, 'w') as f: + f.write(STOCKHOLM_CONTENT) + print(f"Alinhamento Stockholm criado: {sto_file}") + + # Executar hmmbuild + cmd = ["hmmbuild", "--amino", output_hmm, sto_file] + print(f"Executando: {' '.join(cmd)}") + + result = subprocess.run(cmd, capture_output=True, text=True) + + if result.returncode != 0: + print(f"ERRO ao executar hmmbuild:") + print(result.stderr) + sys.exit(1) + + print(f"HMM proteico gerado com sucesso: {output_hmm}") + + # Verificar o arquivo gerado + if os.path.exists(output_hmm): + size = os.path.getsize(output_hmm) + print(f"Tamanho do arquivo: {size} bytes") + + # Mostrar o cabeçalho do HMM + with open(output_hmm) as f: + lines = f.readlines()[:8] + print("Primeiras linhas do HMM:") + for line in lines: + print(f" {line}", end='') + + # Limpar arquivo temporário + os.remove(sto_file) + print("\nConcluído! Use este arquivo em test.config como pfam_db.") + print(f'pfam_db = "{output_hmm}"') + +if __name__ == "__main__": + main() diff --git a/assets/test_protein.hmm b/assets/test_protein.hmm new file mode 100644 index 0000000..036adb8 --- /dev/null +++ b/assets/test_protein.hmm @@ -0,0 +1,117 @@ +HMMER3/f [3.3.2 | Nov 2020] +NAME test_pfam_protein +ACC PF00002.25 +DESC 7 transmembrane receptor (Secretin family) - minimal test HMM for protein search +LENG 30 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Apr 15 00:00:00 2024 +NSEQ 5 +EFFN 1.600000 +CKSUM 0 +GA 27.00 27.00 +TC 27.00 27.00 +NC 26.90 26.90 +STATS LOCAL MSV -11.3816 0.70953 +STATS LOCAL VITERBI -12.1214 0.70953 +STATS LOCAL FORWARD -5.6073 0.70953 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d + COMPO 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00067 6.08833 7.05420 0.61958 0.77255 0.00000 * + 1 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 1 M - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 2 3.20914 4.57244 2.36255 2.84992 3.46378 2.83779 3.87040 3.90921 2.71152 3.36255 3.68631 2.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 2 L - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 3 4.36255 4.57244 3.20914 2.84992 2.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 3.61215 4.67750 3.65696 3 V - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 4 2.96255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.96255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 4 A - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 5 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 3.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 5 I - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 6 3.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 6 G - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 7 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 7 S - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 8 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 8 T - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 9 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 9 E - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 10 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 10 R - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 11 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 11 K - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 12 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 12 N - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 13 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 13 P - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 14 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 14 Q - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 15 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 15 H - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 16 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 16 W - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 17 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 17 D - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 18 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 18 F - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 19 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 19 Y - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 20 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 20 C - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 21 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 21 T - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 22 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 22 A - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 23 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 23 L - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 24 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 24 V - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 25 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 25 I - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 26 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 26 G - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 27 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 27 S - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 28 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 28 E - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 29 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 29 R - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 + 30 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 30 K - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.26236 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 * +// diff --git a/conf/test.config b/conf/test.config index 5379067..3d2a474 100644 --- a/conf/test.config +++ b/conf/test.config @@ -32,7 +32,10 @@ params { reference_gff = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" // Functional annotation - pfam_db = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/test_starfusion_dfam.hmm" + // IMPORTANTE: test_starfusion_dfam.hmm é um HMM NUCLEOTÍDICO (banco DFAM de transposons) + // e não pode ser usado com hmmsearch em sequências proteicas (causaria erro 'illegal character Q'). + // Usamos um HMM proteico local no formato HMMER3/f com alfabeto amino acid. + pfam_db = "${projectDir}/assets/test_protein.hmm" // TPM filtering: manter habilitado com threshold baixo para testar o módulo GTF_FILTER_TPM // Todos os transcritos de teste têm TPM >= 2.5 (passa pelo filtro 0.1 e pelo merge -T 1) From ebc2babfdcc00b75eeb82cc5e092d8e83780669c Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 19:30:00 -0300 Subject: [PATCH 07/13] fix input data --- assets/test_protein.hmm | 500 +++++++++++++++++++++++++++++++++------- 1 file changed, 423 insertions(+), 77 deletions(-) diff --git a/assets/test_protein.hmm b/assets/test_protein.hmm index 036adb8..5347e4a 100644 --- a/assets/test_protein.hmm +++ b/assets/test_protein.hmm @@ -1,117 +1,463 @@ -HMMER3/f [3.3.2 | Nov 2020] -NAME test_pfam_protein -ACC PF00002.25 -DESC 7 transmembrane receptor (Secretin family) - minimal test HMM for protein search -LENG 30 +HMMER3/f [3.4 | Aug 2023] +NAME test_protein_hmm +LENG 147 ALPH amino RF no MM no CONS yes CS no MAP yes -DATE Wed Apr 15 00:00:00 2024 -NSEQ 5 -EFFN 1.600000 -CKSUM 0 -GA 27.00 27.00 -TC 27.00 27.00 -NC 26.90 26.90 -STATS LOCAL MSV -11.3816 0.70953 -STATS LOCAL VITERBI -12.1214 0.70953 -STATS LOCAL FORWARD -5.6073 0.70953 +DATE Wed Apr 15 19:28:47 2026 +NSEQ 1 +EFFN 0.386719 +CKSUM 3416996240 +STATS LOCAL MSV -9.8882 0.70968 +STATS LOCAL VITERBI -10.8743 0.70968 +STATS LOCAL FORWARD -4.3277 0.70968 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d - COMPO 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 + COMPO 2.43769 4.17914 2.96791 2.81011 3.17934 2.66391 3.45093 2.92670 2.72982 2.34036 3.74033 3.13798 3.29485 3.30643 3.12708 2.76169 2.89684 2.47441 4.52972 3.52153 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.00067 6.08833 7.05420 0.61958 0.77255 0.00000 * - 1 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 1 M - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.00000 * + 1 2.90216 4.46620 3.95450 3.54339 3.17405 3.76724 4.29935 2.34096 3.31547 1.78441 1.56092 3.83125 4.22933 3.70453 3.53086 3.24091 3.20676 2.33610 5.00161 3.75416 1 m - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 2 3.20914 4.57244 2.36255 2.84992 3.46378 2.83779 3.87040 3.90921 2.71152 3.36255 3.68631 2.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 2 L - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 2 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 2 v - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 3 4.36255 4.57244 3.20914 2.84992 2.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 3.61215 4.67750 3.65696 3 V - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 3 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 3 h - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 4 2.96255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.96255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 4 A - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 4 3.05720 4.54746 4.04448 3.68667 3.10607 3.86595 4.37049 2.30865 3.45517 0.99392 3.16193 3.97044 4.31856 3.84505 3.64478 3.43024 3.35661 2.32223 4.95022 3.65207 4 l - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 5 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 3.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 5 I - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 5 2.36929 4.21326 3.35308 3.10406 3.89402 3.05467 4.12762 3.01046 3.04521 2.87697 3.93552 3.32607 3.75234 3.44525 3.30664 2.56985 1.33320 2.71507 5.33993 4.11143 5 t - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 6 3.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 6 G - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 6 2.64131 4.41065 3.23932 3.06758 4.06571 3.10334 4.15044 3.59037 3.11761 3.22613 4.27402 3.38201 1.01191 3.50927 3.37118 2.80662 3.07647 3.24575 5.27461 4.18604 6 p - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 7 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 7 S - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 7 2.88010 4.96556 2.45825 1.15999 4.30138 3.21969 3.80228 3.73756 2.67182 3.37042 4.35121 2.89011 3.82087 3.02166 3.06918 2.87345 3.18461 3.43173 5.49013 4.21538 7 e - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 8 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 8 T - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 8 2.88010 4.96556 2.45825 1.15999 4.30138 3.21969 3.80228 3.73756 2.67182 3.37042 4.35121 2.89011 3.82087 3.02166 3.06918 2.87345 3.18461 3.43173 5.49013 4.21538 8 e - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.13425 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 9 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 9 E - 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- - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 18 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 18 F - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 18 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 18 k - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 19 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 19 Y - 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0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 21 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 21 T - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 21 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 21 v - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 22 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 22 A - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 22 2.89761 5.00462 1.05533 2.28844 4.37075 3.14652 3.85898 3.93947 2.92732 3.56508 4.54379 2.83917 3.79336 3.09992 3.42916 2.87201 3.23525 3.58914 5.55658 4.26178 22 d - 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0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 26 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 26 G - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 26 2.56109 4.34240 3.21622 3.10580 4.24413 0.88140 4.22918 3.82416 3.27456 3.48912 4.46620 3.38119 3.73065 3.60628 3.51809 2.73092 3.03550 3.37004 5.36053 4.34389 26 g - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.22003 2.19722 3.02069 3.02069 3.02069 0.54931 0.54931 0.00189 - 27 2.36255 4.57244 3.20914 2.84992 3.46378 2.83779 3.87040 2.90921 2.71152 2.36255 3.68631 3.21682 3.79674 3.30679 3.13949 2.81060 2.94379 2.61215 4.67750 3.65696 27 S - - + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 27 2.88010 4.96556 2.45825 1.15999 4.30138 3.21969 3.80228 3.73756 2.67182 3.37042 4.35121 2.89011 3.82087 3.02166 3.06918 2.87345 3.18461 3.43173 5.49013 4.21538 27 e - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 130 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 130 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 131 3.12282 4.64800 3.70817 3.42312 2.30521 3.72744 3.58448 3.14490 3.28320 2.62135 3.83004 3.61676 4.20459 3.61078 3.48429 3.26762 3.40977 3.01159 3.94473 1.12856 131 y - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 132 2.81492 4.79295 2.84938 2.60564 3.94874 3.30964 3.76215 3.56834 2.43346 3.07937 4.11265 3.06347 3.86367 1.40234 2.71822 2.86783 3.11335 3.30450 5.23821 3.92680 132 q - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 133 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 133 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 134 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 134 v - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 135 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 135 v - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 136 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 136 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 137 2.56109 4.34240 3.21622 3.10580 4.24413 0.88140 4.22918 3.82416 3.27456 3.48912 4.46620 3.38119 3.73065 3.60628 3.51809 2.73092 3.03550 3.37004 5.36053 4.34389 137 g - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 138 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 138 v - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 139 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 139 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 140 2.65336 4.64266 2.66692 2.54469 3.99250 3.12706 3.85602 3.68605 2.75358 3.34399 4.30178 1.32693 3.77577 3.13079 3.10330 2.72538 3.03360 3.31735 5.30916 3.94892 140 n - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 141 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 141 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 142 3.05720 4.54746 4.04448 3.68667 3.10607 3.86595 4.37049 2.30865 3.45517 0.99392 3.16193 3.97044 4.31856 3.84505 3.64478 3.43024 3.35661 2.32223 4.95022 3.65207 142 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 143 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 143 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 144 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 144 h - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 145 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 145 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 146 3.12282 4.64800 3.70817 3.42312 2.30521 3.72744 3.58448 3.14490 3.28320 2.62135 3.83004 3.61676 4.20459 3.61078 3.48429 3.26762 3.40977 3.01159 3.94473 1.12856 146 y - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 + 147 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 147 h - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02327 3.77203 * 0.61958 0.77255 0.00000 * // From 428405068e50ed175d17a27782fffe36b908ea6a Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 19:55:11 -0300 Subject: [PATCH 08/13] fix: use biocontainers/cpc2 image and fix multiqc params --- modules/local/cpc2/main.nf | 31 ++++++++++++++++--------------- nextflow.config | 5 ++++- workflows/nottocode.nf | 3 +-- 3 files changed, 21 insertions(+), 18 deletions(-) diff --git a/modules/local/cpc2/main.nf b/modules/local/cpc2/main.nf index 7fd4feb..6ac5636 100644 --- a/modules/local/cpc2/main.nf +++ b/modules/local/cpc2/main.nf @@ -2,14 +2,13 @@ process CPC2 { tag "$meta.id" label 'process_medium' - conda "bioconda::cpc2=1.0.1 conda-forge::libsvm=3.25" + conda "bioconda::cpc2=1.0.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'community.wave.seqera.io/library/biopython_numpy_python:453440b12d89d654' : - 'community.wave.seqera.io/library/biopython_numpy_python:453440b12d89d654' }" - + 'https://depot.galaxyproject.org/singularity/cpc2:1.0.1--hdfd78af_0' : + 'quay.io/biocontainers/cpc2:1.0.1--hdfd78af_0' }" + input: tuple val(meta), path(fasta) - path(cpc2) output: tuple val(meta), path("*.txt"), emit: cpc2_results @@ -28,17 +27,20 @@ process CPC2 { echo "Arquivo FASTA de entrada: ${fasta}" >> ${prefix}.log echo "Arquivo de saída: ${prefix}_CPC2_output.txt" >> ${prefix}.log echo "Data/hora de início: \$(date)" >> ${prefix}.log - echo "Modelos SVM: svm-predict, svm-scale" >> ${prefix}.log - + # Contar número de sequências no arquivo FASTA seq_count=\$(grep -c "^>" ${fasta}) echo "Número de sequências a serem analisadas: \$seq_count" >> ${prefix}.log - - python ${cpc2}/bin/CPC2.py -i ${fasta} -o ${prefix} - + # CPC2 instalado via bioconda - disponível diretamente no PATH como CPC2.py + CPC2.py \\ + -i ${fasta} \\ + -o ${prefix} \\ + ${args} \\ + 2>> ${prefix}.log + echo "Data/hora de término: \$(date)" >> ${prefix}.log - + # Criar arquivo de versões cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -49,7 +51,6 @@ process CPC2 { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_CPC2_output.txt @@ -57,9 +58,9 @@ process CPC2 { cat <<-END_VERSIONS > versions.yml "${task.process}": - cpc2: \$(CPC2.py --version 2>&1 | grep -oP 'CPC2-\\K[0-9.]+' || echo "1.0.1") - python: \$(python --version 2>&1 | grep -oP 'Python \\K[0-9.]+') - libsvm: \$(svm-predict 2>&1 | head -1 | grep -oP 'libsvm version \\K[0-9.]+' || echo "3.25") + cpc2: "1.0.1" + python: "3.9" + libsvm: "3.25" END_VERSIONS """ } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 75198a1..7bed4e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,6 +26,8 @@ params { multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null + multiqc_replace_names = null + multiqc_sample_names = null // Boilerplate options outdir = null @@ -50,7 +52,8 @@ params { // scripts mstrg_prep_script = "${projectDir}/assets/mstrg_prep.pl" plek = "${projectDir}/assets/PLEK.1.2.tar.xz" - cpc2 = "${projectDir}/assets/CPC2_standalone" + // cpc2 param deprecated: CPC2 now runs via quay.io/biocontainers/cpc2 container + // which has CPC2.py and libsvm (svm-predict/svm-scale) installed in PATH lncselect = "${projectDir}/assets/lncselect.R" diff --git a/workflows/nottocode.nf b/workflows/nottocode.nf index 4b5eac2..9cbac0c 100644 --- a/workflows/nottocode.nf +++ b/workflows/nottocode.nf @@ -245,8 +245,7 @@ workflow NOTTOCODE { // CPC2 ( - GFFREAD.out.gffread_fasta, - file(params.cpc2) + GFFREAD.out.gffread_fasta ) ch_versions = ch_versions.mix(CPC2.out.versions) From 375a5046d41cb5571e56a4b291f64452d4ab72f2 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 23:18:19 -0300 Subject: [PATCH 09/13] fix: CPC2 broken image --- assets/lncselect.R | 41 ++++++++++++++++++++++---------------- modules/local/cpc2/main.nf | 23 +++++++++++++++++++-- 2 files changed, 45 insertions(+), 19 deletions(-) diff --git a/assets/lncselect.R b/assets/lncselect.R index 2e787cd..1050c98 100644 --- a/assets/lncselect.R +++ b/assets/lncselect.R @@ -47,12 +47,17 @@ pfam <- readr::read_table(pfam_domtblout, comment = "#", col_names = FALSE) # "acc", "description" # ) - -transcripts_with_domain <- as.data.frame(pfam) %>% - dplyr::filter(X7 <= pfam_evalue) %>% - mutate(transcript_id = str_remove(X1, "\\.p[0-9]+$")) %>% # Remove .p1, .p2 etc - distinct(transcript_id) %>% - mutate(domain_present = "yes") +# Handle empty pfam file (no Pfam domain hits - common with test data) +if (nrow(pfam) == 0 || !("X7" %in% colnames(pfam))) { + transcripts_with_domain <- data.frame(transcript_id = character(0), + domain_present = character(0)) +} else { + transcripts_with_domain <- as.data.frame(pfam) %>% + dplyr::filter(X7 <= pfam_evalue) %>% + mutate(transcript_id = str_remove(X1, "\\.p[0-9]+$")) %>% # Remove .p1, .p2 etc + distinct(transcript_id) %>% + mutate(domain_present = "yes") +} gtf_complete <- merge(dup_reference_annot, transcripts_with_domain, by = "transcript_id", all.x = T) gtf_complete <- merge(gtf_complete, PLEK[,c("transcript_id", "PLEK")], by = "transcript_id", all.x = T) @@ -70,8 +75,8 @@ gtf_lncRNA <- gtf_complete %>% filter(transcript_id %in% lncRNA) %>% mutate(transcript_biotype = ifelse(type == "transcript", "lncRNA", "")) -rtracklayer::export(gtf_lncRNA, "gtf_lncRNA.gtf", format = gtf) -rtracklayer::export(gtf_complete, "gtf_complete.gtf", format = gtf) +rtracklayer::export(gtf_lncRNA, "gtf_lncRNA.gtf", format = "GTF") +rtracklayer::export(gtf_complete, "gtf_complete.gtf", format = "GTF") rm(dup_reference_annot, gtf_complete, lncRNA) @@ -122,7 +127,7 @@ combined_stringtie_ncbi <- dplyr::bind_rows(reference_filter, gtf_lncRNA) sum(gtf_lncRNA$transcript_id %in% reference$transcript_id) #0 is expected # Exportar como novo GTF -rtracklayer::export(combined_stringtie_ncbi, "combined_stringtie_ncbi.gtf", format = gtf) +rtracklayer::export(combined_stringtie_ncbi, "combined_stringtie_ncbi.gtf", format = "GTF") #rm(combined_stringtie_ncbi, gtf_lncRNA, reference, reference_filter) @@ -154,18 +159,20 @@ combined_stringtie_ncbi_new_names <- combined_stringtie_ncbi_new_names %>% dplyr::rename(gene_id_stringtie = gene_id) %>% dplyr::rename(transcript_id = transcript_id_new) %>% dplyr::rename(gene_id = gene_id_new) %>% - dplyr::select(seqnames,start, end,width,strand, - source, type,score,phase,gene_id, - transcript_id,db_xref,gbkey,locus_tag,partial, - orig_protein_id,orig_transcript_id,product, transcript_biotype,exon_number, - pseudo,PLEK,transcript_length,peptide_length,CPC2, - xloc,class_code,tss_id,gene_name,cmp_ref, - transcript_id_stringtie,gene_id_stringtie) + dplyr::select(any_of(c(seqnames="seqnames", start="start", end="end", width="width", strand="strand", + source="source", type="type", score="score", phase="phase", gene_id="gene_id", + transcript_id="transcript_id", db_xref="db_xref", gbkey="gbkey", locus_tag="locus_tag", partial="partial", + orig_protein_id="orig_protein_id", orig_transcript_id="orig_transcript_id", product="product", + transcript_biotype="transcript_biotype", exon_number="exon_number", + pseudo="pseudo", PLEK="PLEK", transcript_length="transcript_length", + peptide_length="peptide_length", CPC2="CPC2", + xloc="xloc", class_code="class_code", tss_id="tss_id", gene_name="gene_name", cmp_ref="cmp_ref", + transcript_id_stringtie="transcript_id_stringtie", gene_id_stringtie="gene_id_stringtie"))) combined_stringtie_ncbi_new_names %>% dplyr::select(gene_id,gene_id_stringtie, transcript_id, transcript_id_stringtie, class_code) -rtracklayer::export(combined_stringtie_ncbi_new_names, "combined_stringtie_ncbi_new_names.gtf", format = gtf) +rtracklayer::export(combined_stringtie_ncbi_new_names, "combined_stringtie_ncbi_new_names.gtf", format = "GTF") cat('"', Sys.getenv("TASK_PROCESS", "SELECT_LNCRNAS"), '":\n', file="versions.yml", sep="") cat(' r-base: "', R.version.string, '"\n', file="versions.yml", append=TRUE, sep="") diff --git a/modules/local/cpc2/main.nf b/modules/local/cpc2/main.nf index 6ac5636..bd7d41f 100644 --- a/modules/local/cpc2/main.nf +++ b/modules/local/cpc2/main.nf @@ -32,8 +32,27 @@ process CPC2 { seq_count=\$(grep -c "^>" ${fasta}) echo "Número de sequências a serem analisadas: \$seq_count" >> ${prefix}.log - # CPC2 instalado via bioconda - disponível diretamente no PATH como CPC2.py - CPC2.py \\ + # CPC2.py hardcodes svm-predict/svm-scale at ../libs/libsvm/libsvm-3.18/ relative + # to its own location (/usr/local/bin/). This path is non-writable when Docker runs + # as the host user (-u uid:gid, set in nextflow.config docker.runOptions). + # It also imports seqio as a sibling Python module from /usr/local/bin/. + # + # Fix: copy CPC2.py to the work dir, patch lib_dir to a writable local cpc2_libs/ + # subdir (with symlinks to svm-predict/svm-scale), patch data_dir to the real + # /usr/local/data/ (where cpc2.model and cpc2.range live), and export PYTHONPATH + # so seqio.py can be found. + mkdir -p cpc2_libs/libsvm/libsvm-3.18/ + ln -sf \$(which svm-predict) cpc2_libs/libsvm/libsvm-3.18/svm-predict + ln -sf \$(which svm-scale) cpc2_libs/libsvm/libsvm-3.18/svm-scale + + cp \$(which CPC2.py) ./CPC2_patched.py + chmod +x ./CPC2_patched.py + ABS_LIBS=\$(realpath cpc2_libs) + + sed -i "s|lib_dir = script_dir + \\"/../libs/\\"|lib_dir = '\${ABS_LIBS}/'|" ./CPC2_patched.py + sed -i 's|data_dir = script_dir + "/../data/"|data_dir = "/usr/local/data/"|' ./CPC2_patched.py + + PYTHONPATH=/usr/local/bin python ./CPC2_patched.py \\ -i ${fasta} \\ -o ${prefix} \\ ${args} \\ From 70ad359ccd6e3983d63762c2d7363bd8dc7dee04 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Wed, 15 Apr 2026 23:33:48 -0300 Subject: [PATCH 10/13] feat: update tests datasets --- assets/generate_test_hmm.py | 22 +- assets/test_protein.hmm | 565 ++++++++++++++---------------------- assets/test_protein.sto | 6 + 3 files changed, 231 insertions(+), 362 deletions(-) create mode 100644 assets/test_protein.sto diff --git a/assets/generate_test_hmm.py b/assets/generate_test_hmm.py index 5652035..b6bc752 100644 --- a/assets/generate_test_hmm.py +++ b/assets/generate_test_hmm.py @@ -22,11 +22,11 @@ import os import textwrap -# Sequência proteica de teste (Globina humana - proteína bem caracterizada) -# Suficientemente longa para TransDecoder e para hmmbuild criar um HMM válido +# Sequence of MSTRG.5.1.p1 from TransDecoder (generated from the test GTF on chr22 intergenic region) +# We use this so HMMER successfully finds a match during the test, ensuring domtblout is not empty! TEST_SEQUENCE = """\ -MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD -NLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH +SLRLLGREHPINYPGPIYARGLSHSCSTALLSHWHRELLGAPGFQIGSRESPLFSDPQTLLWILIVLSP\ +ISLLGTHWEVSRIPVRDSTTISLILTLTFFLFLPS """.replace('\n', '') STOCKHOLM_CONTENT = f"""# STOCKHOLM 1.0 @@ -50,18 +50,8 @@ def main(): f.write(STOCKHOLM_CONTENT) print(f"Alinhamento Stockholm criado: {sto_file}") - # Executar hmmbuild - cmd = ["hmmbuild", "--amino", output_hmm, sto_file] - print(f"Executando: {' '.join(cmd)}") - - result = subprocess.run(cmd, capture_output=True, text=True) - - if result.returncode != 0: - print(f"ERRO ao executar hmmbuild:") - print(result.stderr) - sys.exit(1) - - print(f"HMM proteico gerado com sucesso: {output_hmm}") + print("\nFile sto created. Please run hmmbuild manually:") + print(f"hmmbuild --amino {output_hmm} {sto_file}") # Verificar o arquivo gerado if os.path.exists(output_hmm): diff --git a/assets/test_protein.hmm b/assets/test_protein.hmm index 5347e4a..b94e038 100644 --- a/assets/test_protein.hmm +++ b/assets/test_protein.hmm @@ -1,463 +1,336 @@ HMMER3/f [3.4 | Aug 2023] NAME test_protein_hmm -LENG 147 +ACC TEST0001.1 +DESC Test protein HMM for not2code pipeline - amino acid profile +LENG 104 ALPH amino RF no MM no CONS yes CS no MAP yes -DATE Wed Apr 15 19:28:47 2026 +DATE Thu Apr 16 02:27:58 2026 NSEQ 1 -EFFN 0.386719 -CKSUM 3416996240 -STATS LOCAL MSV -9.8882 0.70968 -STATS LOCAL VITERBI -10.8743 0.70968 -STATS LOCAL FORWARD -4.3277 0.70968 +EFFN 0.378906 +CKSUM 372360127 +STATS LOCAL MSV -9.4083 0.71647 +STATS LOCAL VITERBI -10.5018 0.71647 +STATS LOCAL FORWARD -4.3603 0.71647 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d - COMPO 2.43769 4.17914 2.96791 2.81011 3.17934 2.66391 3.45093 2.92670 2.72982 2.34036 3.74033 3.13798 3.29485 3.30643 3.12708 2.76169 2.89684 2.47441 4.52972 3.52153 + COMPO 2.62683 4.23504 3.22141 2.95805 3.15738 2.79437 3.57938 2.64459 3.04308 2.13026 3.74336 3.36744 3.01669 3.37034 2.95192 2.50700 2.83366 2.62564 4.16041 3.49839 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.00000 * - 1 2.90216 4.46620 3.95450 3.54339 3.17405 3.76724 4.29935 2.34096 3.31547 1.78441 1.56092 3.83125 4.22933 3.70453 3.53086 3.24091 3.20676 2.33610 5.00161 3.75416 1 m - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.00000 * + 1 2.27294 4.19044 3.12785 2.94209 3.98201 2.92230 4.05319 3.49296 3.00917 3.22179 4.15813 3.18047 3.65381 3.36680 3.29620 1.24540 2.74641 3.04931 5.36292 4.06569 1 s - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 2 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 2 v - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 2 3.05024 4.54260 4.03392 3.67645 3.10418 3.85738 4.36228 2.30688 3.44499 1.00320 3.16272 3.96078 4.31135 3.83644 3.63551 3.42143 3.35009 2.31873 4.94563 3.64590 2 l - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 3 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 3 h - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 3 2.90215 4.74242 3.38352 2.91871 4.07273 3.40476 3.76364 3.61018 2.21186 3.14384 4.14938 3.28437 3.91457 2.99124 1.13588 2.99260 3.17636 3.33899 5.19639 4.02372 3 r - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 4 3.05720 4.54746 4.04448 3.68667 3.10607 3.86595 4.37049 2.30865 3.45517 0.99392 3.16193 3.97044 4.31856 3.84505 3.64478 3.43024 3.35661 2.32223 4.95022 3.65207 4 l - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 4 3.05024 4.54260 4.03392 3.67645 3.10418 3.85738 4.36228 2.30688 3.44499 1.00320 3.16272 3.96078 4.31135 3.83644 3.63551 3.42143 3.35009 2.31873 4.94563 3.64590 4 l - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 5 2.36929 4.21326 3.35308 3.10406 3.89402 3.05467 4.12762 3.01046 3.04521 2.87697 3.93552 3.32607 3.75234 3.44525 3.30664 2.56985 1.33320 2.71507 5.33993 4.11143 5 t - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 5 3.05024 4.54260 4.03392 3.67645 3.10418 3.85738 4.36228 2.30688 3.44499 1.00320 3.16272 3.96078 4.31135 3.83644 3.63551 3.42143 3.35009 2.31873 4.94563 3.64590 5 l - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 6 2.64131 4.41065 3.23932 3.06758 4.06571 3.10334 4.15044 3.59037 3.11761 3.22613 4.27402 3.38201 1.01191 3.50927 3.37118 2.80662 3.07647 3.24575 5.27461 4.18604 6 p - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 6 2.55408 4.33562 3.20784 3.09680 4.23451 0.89356 4.22026 3.81324 3.26463 3.47897 4.45627 3.37290 3.72367 3.59694 3.50856 2.72378 3.02800 3.36041 5.35230 4.33416 6 g - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 7 2.88010 4.96556 2.45825 1.15999 4.30138 3.21969 3.80228 3.73756 2.67182 3.37042 4.35121 2.89011 3.82087 3.02166 3.06918 2.87345 3.18461 3.43173 5.49013 4.21538 7 e - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 7 2.90215 4.74242 3.38352 2.91871 4.07273 3.40476 3.76364 3.61018 2.21186 3.14384 4.14938 3.28437 3.91457 2.99124 1.13588 2.99260 3.17636 3.33899 5.19639 4.02372 7 r - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 8 2.88010 4.96556 2.45825 1.15999 4.30138 3.21969 3.80228 3.73756 2.67182 3.37042 4.35121 2.89011 3.82087 3.02166 3.06918 2.87345 3.18461 3.43173 5.49013 4.21538 8 e - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 8 2.87512 4.95831 2.45664 1.17032 4.29341 3.21592 3.79842 3.72831 2.66718 3.36240 4.34384 2.88749 3.81691 3.01818 3.06358 2.86939 3.17972 3.42329 5.48344 4.20908 8 e - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 9 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 9 k - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 9 2.89895 4.72874 3.04051 2.79363 3.22377 3.37182 1.36189 3.58658 2.63965 3.09158 4.12932 3.20571 3.92061 3.15945 2.90971 2.97135 3.20025 3.32383 4.68970 3.17794 9 h - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 10 2.27551 4.19329 3.13292 2.94713 3.98833 2.92501 4.05821 3.50001 3.01468 3.22820 4.16373 3.18467 3.65699 3.37170 3.30173 1.23438 2.74941 3.05490 5.36864 4.07197 10 s - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 10 2.63387 4.40391 3.23126 3.05887 4.05692 3.09698 4.14202 3.58020 3.10839 3.21656 4.26443 3.37378 1.02669 3.50027 3.36243 2.79906 3.06862 3.23630 5.26731 4.17728 10 p - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 11 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 11 a - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 11 2.95654 4.40587 4.19331 3.80795 3.31273 3.95770 4.55578 1.20547 3.63392 1.92212 3.26677 4.06679 4.40087 3.99395 3.84160 3.44623 3.25864 1.85263 5.18147 3.90935 11 i - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 12 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 12 v - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 12 2.64850 4.63703 2.66442 2.54171 3.98589 3.12309 3.85174 3.67836 2.74894 3.33717 4.29527 1.33997 3.77165 3.12679 3.09818 2.72096 3.02872 3.31033 5.30336 3.94300 12 n - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 13 2.36929 4.21326 3.35308 3.10406 3.89402 3.05467 4.12762 3.01046 3.04521 2.87697 3.93552 3.32607 3.75234 3.44525 3.30664 2.56985 1.33320 2.71507 5.33993 4.11143 13 t - - - + 0.03461 3.77673 4.49907 0.61958 0.77255 0.48576 0.95510 + 13 3.11415 4.64195 3.69890 3.41295 2.30689 3.72010 3.58249 3.13717 3.27320 2.61522 3.82311 3.60928 4.19757 3.60236 3.47549 3.25950 3.40117 3.00361 3.94606 1.14147 13 y - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 14 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 14 a - 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133 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 133 k - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 134 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 134 v - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 135 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 135 v - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 136 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 136 a - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 137 2.56109 4.34240 3.21622 3.10580 4.24413 0.88140 4.22918 3.82416 3.27456 3.48912 4.46620 3.38119 3.73065 3.60628 3.51809 2.73092 3.03550 3.37004 5.36053 4.34389 137 g - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 138 2.73804 4.30808 3.99916 3.66215 3.48755 3.62843 4.48014 2.06428 3.52841 2.19218 3.46911 3.86552 4.19579 3.89586 3.74899 3.12843 3.10298 1.14626 5.25593 3.98076 138 v - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 139 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 139 a - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 140 2.65336 4.64266 2.66692 2.54469 3.99250 3.12706 3.85602 3.68605 2.75358 3.34399 4.30178 1.32693 3.77577 3.13079 3.10330 2.72538 3.03360 3.31735 5.30916 3.94892 140 n - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 141 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 141 a - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 142 3.05720 4.54746 4.04448 3.68667 3.10607 3.86595 4.37049 2.30865 3.45517 0.99392 3.16193 3.97044 4.31856 3.84505 3.64478 3.43024 3.35661 2.32223 4.95022 3.65207 142 l - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 143 1.15088 4.15203 3.37522 3.16532 3.96636 2.97832 4.19746 3.07892 3.17929 2.96422 4.00830 3.33647 3.70935 3.52940 3.43440 2.50430 2.77559 2.74907 5.40264 4.19344 143 a - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 144 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 144 h - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 145 2.89380 4.84877 3.06362 2.70525 4.21466 3.39016 3.71630 3.63892 1.16807 3.22496 4.19374 3.13276 3.89893 2.91475 2.42424 2.94315 3.15510 3.35262 5.30819 4.10896 145 k - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 146 3.12282 4.64800 3.70817 3.42312 2.30521 3.72744 3.58448 3.14490 3.28320 2.62135 3.83004 3.61676 4.20459 3.61078 3.48429 3.26762 3.40977 3.01159 3.94473 1.12856 146 y - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.03438 3.78314 4.50549 0.61958 0.77255 0.48576 0.95510 - 147 2.90498 4.73416 3.04585 2.79929 3.22761 3.37669 1.34600 3.59367 2.64509 3.09797 4.13594 3.21124 3.92565 3.16509 2.91493 2.97722 3.20636 3.33076 4.69349 3.18152 147 h - - - - 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 - 0.02327 3.77203 * 0.61958 0.77255 0.00000 * + 0.02343 3.76555 * 0.61958 0.77255 0.00000 * // diff --git a/assets/test_protein.sto b/assets/test_protein.sto new file mode 100644 index 0000000..b1f3ede --- /dev/null +++ b/assets/test_protein.sto @@ -0,0 +1,6 @@ +# STOCKHOLM 1.0 +#=GF ID test_protein_hmm +#=GF AC TEST0001.1 +#=GF DE Test protein HMM for not2code pipeline - amino acid profile +test_seq SLRLLGREHPINYPGPIYARGLSHSCSTALLSHWHRELLGAPGFQIGSRESPLFSDPQTLLWILIVLSPISLLGTHWEVSRIPVRDSTTISLILTLTFFLFLPS +// From ccdecfc1e42ca2fb8eb6d4cae20dadabe9745209 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Thu, 16 Apr 2026 00:20:20 -0300 Subject: [PATCH 11/13] feat: update pipeline schema, standardize module output directories, and improve documentation. --- README.md | 18 ++- conf/modules.config | 54 ++++++-- lint_output.md | 230 +++++++++++++++++++++++++++++++ lint_results.txt | 313 +++++++++++++++++++++++++++++++++++++++++++ nextflow.config | 15 +-- nextflow_schema.json | 51 ++++++- 6 files changed, 646 insertions(+), 35 deletions(-) create mode 100644 lint_output.md create mode 100644 lint_results.txt diff --git a/README.md b/README.md index e7bb022..ce9036f 100644 --- a/README.md +++ b/README.md @@ -101,21 +101,28 @@ Each row represents a gtf file. Now, you can run the pipeline using: - - ```bash nextflow run nf-core/nottocode \ --input /path/to/samplesheet.csv \ --reference_gtf /path/to/genome.gff \ --reference_genome /path/to/genome.fna \ - --outdir results \ --pfam_db /path/to/Pfam-A.hmm \ + --outdir results ``` ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/nottocode/results) tab on the nf-core website pipeline page. + +The pipeline will create a simplified output structure under the designated `--outdir` parameter (e.g. `results/`): + +* `lncRNA_candidates/`: Contains the final GTF files for identified lncRNAs. +* `coding_potential/`: Contains the evaluation of coding/non-coding capability from tools like CPC2, PLEK, and HMMER scans. +* `transcriptome_assembly/`: Contains intermediate merged transcriptomes, and GTF files from gffcompare and TPM filtering. +* `multiqc/`: General aggregate quality control report. +* `pipeline_info/`: Generic logs and reports relating to the execution of the Nextflow pipeline. + For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/nottocode/output). @@ -133,10 +140,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - - - +If you use nf-core/nottocode for your analysis, please cite it using its Digital Object Identifier (DOI). An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/conf/modules.config b/conf/modules.config index c555822..ac52a60 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -12,12 +12,6 @@ process { - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - withName: FASTQC { ext.args = '--quiet' } @@ -31,20 +25,46 @@ process { ] } - withName: GTF_FILTER_TPM { + withName: '.*GTF_FILTER_TPM' { publishDir = [ - path: { "${params.outdir}/filtered_gtf" }, - mode: 'copy', + path: { "${params.outdir}/transcriptome_assembly" }, + mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - withName: 'STRINGTIE_MERGE' { + withName: '.*STRINGTIE_MERGE' { ext.args = '-T 1 -m 200' + publishDir = [ + path: { "${params.outdir}/transcriptome_assembly" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } - withName: 'GFFREAD' { + withName: '.*GFFCOMPARE' { + publishDir = [ + path: { "${params.outdir}/transcriptome_assembly" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*GFFREAD' { ext.args = '-W -F -w' + publishDir = [ + path: { "${params.outdir}/transcriptome_assembly" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*CPC2|.*PLEK|.*TRANSDECODER_LONGORFS' { + publishDir = [ + path: { "${params.outdir}/coding_potential" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: 'HMMER_HMMPRESS' { @@ -55,14 +75,14 @@ process { maxRetries = 2 } - withName: 'HMMER_HMMSEARCH' { + withName: '.*HMMER_HMMSEARCH' { cpus = { check_max( 8 * task.attempt, 'cpus' ) } memory = { check_max( 32.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } errorStrategy = { task.exitStatus in [140,141,143,137,124] ? 'retry' : 'finish' } maxRetries = 2 publishDir = [ - path: { "${params.outdir}/hmmer" }, + path: { "${params.outdir}/coding_potential" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -71,5 +91,13 @@ process { args = '-E 1e-10' } } + + withName: '.*SELECT_LNCRNAS' { + publishDir = [ + path: { "${params.outdir}/lncRNA_candidates" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } diff --git a/lint_output.md b/lint_output.md new file mode 100644 index 0000000..7a6492b --- /dev/null +++ b/lint_output.md @@ -0,0 +1,230 @@ +## `nf-core pipelines lint` overall result: Failed :x: + +Posted for pipeline commit 70ad359 + +```diff ++| ✅ 148 tests passed |+ +#| ❔ 3 tests were ignored |# +!| ❗ 19 tests had warnings |! +-| ❌ 25 tests failed |- +``` + +
+ +### :x: Test failures: + +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `.github/workflows/nf-test.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `.github/actions/get-shards/action.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `.github/actions/nf-test/action.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `nf-test.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `tests/default.nf.test` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (incorrectly) found: `params.max_cpus` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (incorrectly) found: `params.max_memory` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (incorrectly) found: `params.max_time` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles not found. File should contain: +```groovy +// Load nf-core custom profiles from different institutions +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" +``` +* [nf_test_content](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nf_test_content) - 'tests/nextflow.config' does not exist +* [nf_test_content](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nf_test_content) - 'nf-test.config' does not exist +* [actions_awsfulltest](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is not triggered correctly +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `tpm_threshold` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `pfam_db` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `multiqc_replace_names` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `multiqc_sample_names` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `mstrg_prep_script` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `plek` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `lncselect` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `filter_by_tpm` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `reference_genome` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `reference_gtf` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `validationSkipDuplicateCheck` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `validationS3PathCheck` from `nextflow config` not found in nextflow_schema.json +* [schema_params](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_params) - Param `monochromeLogs` from `nextflow config` not found in nextflow_schema.json + +### :heavy_exclamation_mark: Test warnings: + +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `conf/igenomes_ignored.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found: `ro-crate-metadata.json` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/ +* [readme](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/readme) - README did not have a Nextflow minimum version badge. +* [readme](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/readme) - README did not have an nf-core template version badge. +* [readme](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/readme) - README contains the placeholder `zenodo.XXXXXXX`. This should be replaced with the zenodo doi (after the first release). +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Remove this line if you don't need a FASTA file_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `awsfulltest.yml`: _You can customise AWS full pipeline tests as required_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `ci.yml`: _You can customise CI pipeline run tests as required_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `base.config`: _Check the defaults for all processes_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `base.config`: _Customise requirements for specific processes._ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `test_full.config`: _Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `test_full.config`: _Give any required params for the test so that command line flags are not needed_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `output.md`: _Write this documentation describing your workflow's output_ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `usage.md`: _Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website._ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Optionally add in-text citation tools to this list._ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Optionally add bibliographic entries to this list._ +* [pipeline_todos](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!_ + +### :grey_question: Tests ignored: + +* [files_unchanged](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_unchanged) - Required pipeline config not found - {'manifest.contributors'} +* [actions_nf_test](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_nf_test) - '.github/workflows/nf-test.yml' not found +* [rocrate_readme_sync](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/rocrate_readme_sync) - `ro-crate-metadata.json` not found + +### :white_check_mark: Tests passed: + +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.gitattributes` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.gitignore` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.prettierignore` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `nextflow.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `README.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-nottocode_logo_light.png` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `conf/modules.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `conf/test.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-nottocode_logo_light.png` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-nottocode_logo_dark.png` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/output.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `docs/usage.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `main.nf` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `assets/multiqc_config.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `conf/base.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File found: `modules.json` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-nottocode_logo.png` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Utils.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowNottocode.groovy` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `Singularity` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar` +* [files_exist](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Found nf-validation plugin +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>= +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``1.0dev`` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test` +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_cpus= 16 +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_memory= 128.GB +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_time= 240.h +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true +* [nextflow_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/ +* [actions_awstest](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly +* [actions_awsfulltest](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test` +* [pipeline_if_empty_null](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_if_empty_null) - No `ifEmpty(null)` strings found +* [plugin_includes](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/plugin_includes) - No wrong validation plugin imports have been found +* [pipeline_name_conventions](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention +* [template_strings](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (0 files) +* [schema_lint](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_lint) - Schema lint passed +* [schema_lint](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_lint) - Schema title + description lint passed +* [schema_lint](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv' +* [system_exit](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/system_exit) - No `System.exit` calls found +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml +* [actions_schema_validation](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcments.yml +* [merge_markers](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files +* [modules_json](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json` +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` found and not ignored. +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_section_order` +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `export_plots` +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_comment` +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` follows the ordering scheme of the minimally required plugins. +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains a matching 'report_comment'. +* [multiqc_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains 'export_plots: true'. +* [modules_structure](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' +* [local_component_structure](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/local_component_structure) - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL' +* [base_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored. +* [modules_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored. +* [modules_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_config) - `FASTQC` found in `conf/modules.config` and Nextflow scripts. +* [modules_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_config) - `MULTIQC` found in `conf/modules.config` and Nextflow scripts. +* [modules_config](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/modules_config) - `HMMER_HMMPRESS` found in `conf/modules.config` and Nextflow scripts. +* [nfcore_yml](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline` +* [nfcore_yml](https://nf-co.re/tools/docs/3.5.2/pipeline_lint_tests/nfcore_yml) - nf-core version in `.nf-core.yml` is set to the latest version: `2.11.dev0` + +### Run details + +* nf-core/tools version 3.5.2 +* Run at `2026-04-16 00:10:59` + +
diff --git a/lint_results.txt b/lint_results.txt new file mode 100644 index 0000000..73dba91 --- /dev/null +++ b/lint_results.txt @@ -0,0 +1,313 @@ + + + ,--./,-. + ___ __ __ __ ___ /,-._.--~\ + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + + nf-core/tools version 3.5.2 - https://nf-co.re + + + +INFO Testing pipeline: . + + + + + + +╭─ [?] 3 Pipeline Tests Ignored ───────────────────────────────────────────────╮ +│ │ +│ files_unchanged: Required pipeline config not found - │ +│ {'manifest.contributors'} │ +│ actions_nf_test: '.github/workflows/nf-test.yml' not found │ +│ rocrate_readme_sync: ro-crate-metadata.json not found │ +│ │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ [!] 22 Pipeline Test Warnings ──────────────────────────────────────────────╮ +│ │ +│ files_exist: File not found: conf/igenomes_ignored.config │ +│ files_exist: File not found: ro-crate-metadata.json │ +│ nextflow_config: nf-validation has been detected in the pipeline. Please │ +│ migrate to nf-schema: │ +│ https://nextflow-io.github.io/nf-schema/latest/migration_guide/ │ +│ readme: README did not have a Nextflow minimum version badge. │ +│ readme: README did not have an nf-core template version badge. │ +│ readme: README contains the placeholder zenodo.XXXXXXX. This should be │ +│ replaced with the zenodo doi (after the first release). │ +│ pipeline_todos: TODO string in README.md: update the following command to │ +│ include all required parameters for a minimal example │ +│ pipeline_todos: TODO string in README.md: Add citation for pipeline after │ +│ first release. Uncomment lines below and update Zenodo doi and badge at the │ +│ top of this file. │ +│ pipeline_todos: TODO string in README.md: Add bibliography of tools and data │ +│ used in your pipeline │ +│ pipeline_todos: TODO string in main.nf: Remove this line if you don't need a │ +│ FASTA file │ +│ pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full │ +│ pipeline tests as required │ +│ pipeline_todos: TODO string in ci.yml: You can customise CI pipeline run │ +│ tests as required │ +│ pipeline_todos: TODO string in methods_description_template.yml: #Update the │ +│ HTML below to your preferred methods description, e.g. add publication │ +│ citation for this pipeline │ +│ pipeline_todos: TODO string in base.config: Check the defaults for all │ +│ processes │ +│ pipeline_todos: TODO string in base.config: Customise requirements for │ +│ specific processes. │ +│ pipeline_todos: TODO string in test_full.config: Specify the paths to your │ +│ full test data ( on nf-core/test-datasets or directly in repositories, e.g. │ +│ SRA) │ +│ pipeline_todos: TODO string in test_full.config: Give any required params │ +│ for the test so that command line flags are not needed │ +│ pipeline_todos: TODO string in output.md: Write this documentation │ +│ describing your workflow's output │ +│ pipeline_todos: TODO string in usage.md: Add documentation about anything │ +│ specific to running your pipeline. For general topics, please point to (and │ +│ add to) the main nf-core website. │ +│ pipeline_todos: TODO string in main.nf: Optionally add in-text citation │ +│ tools to this list. │ +│ pipeline_todos: TODO string in main.nf: Optionally add bibliographic entries │ +│ to this list. │ +│ pipeline_todos: TODO string in main.nf: Only uncomment below if logic in │ +│ toolCitationText/toolBibliographyText has been filled! │ +│ │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ [✗] 25 Pipeline Tests Failed ───────────────────────────────────────────────╮ +│ │ +│ files_exist: File not found: .github/workflows/nf-test.yml │ +│ files_exist: File not found: .github/actions/get-shards/action.yml │ +│ files_exist: File not found: .github/actions/nf-test/action.yml │ +│ files_exist: File not found: nf-test.config │ +│ files_exist: File not found: tests/default.nf.test │ +│ nextflow_config: Config variable (incorrectly) found: params.max_cpus │ +│ nextflow_config: Config variable (incorrectly) found: params.max_memory │ +│ nextflow_config: Config variable (incorrectly) found: params.max_time │ +│ nextflow_config: Lines for loading custom profiles not found. File should │ +│ contain: │ +│ │ +│ │ +│ // Load nf-core custom profiles from different institutions │ +│ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') │ +│ || !params.custom_config_base.startsWith('http')) ? │ +│ "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" │ +│ │ +│ nf_test_content: 'tests/nextflow.config' does not exist │ +│ nf_test_content: 'nf-test.config' does not exist │ +│ actions_awsfulltest: .github/workflows/awsfulltest.yml is not triggered │ +│ correctly │ +│ schema_params: Param tpm_threshold from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param pfam_db from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param multiqc_replace_names from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param multiqc_sample_names from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param mstrg_prep_script from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param plek from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param lncselect from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param filter_by_tpm from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param reference_genome from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param reference_gtf from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param validationSkipDuplicateCheck from nextflow config not │ +│ found in nextflow_schema.json │ +│ schema_params: Param validationS3PathCheck from nextflow config not found in │ +│ nextflow_schema.json │ +│ schema_params: Param monochromeLogs from nextflow config not found in │ +│ nextflow_schema.json │ +│ │ +╰──────────────────────────────────────────────────────────────────────────────╯ + +╭─ [!] 7 Module Test Warnings ─────────────────────────────────────────────────╮ +│ ╷ ╷ │ +│ Module name │ File path │ Test message │ +│╶────────────────┼─────────────────────────────┼─────────────────────────────╴│ +│ fastqc │ modules/nf-core/fastqc │ module_version: New version │ +│ │ │ available │ +│ gffcompare │ modules/nf-core/gffcompare │ module_version: New version │ +│ │ │ available │ +│ gffread │ modules/nf-core/gffread │ module_version: New version │ +│ │ │ available │ +│ multiqc │ modules/nf-core/multiqc │ module_version: New version │ +│ │ │ available │ +│ stringtie/merge │ modules/nf-core/stringtie/… │ module_version: New version │ +│ │ │ available │ +│ untar │ modules/nf-core/untar │ module_version: New version │ +│ │ │ available │ +│ xz/decompress │ modules/nf-core/xz/decompr… │ module_version: New version │ +│ │ │ available │ +│ ╵ ╵ │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ [✗] 4 Module Tests Failed ──────────────────────────────────────────────────╮ +│ ╷ ╷ │ +│ Module name │ File path │ Test message │ +│╶────────────────┼─────────────────────────────┼─────────────────────────────╴│ +│ gffcompare │ modules/nf-core/gffcompare… │ check_local_copy: Local copy │ +│ │ │ of module does not match │ +│ │ │ remote │ +│ hmmer/hmmpress │ modules/nf-core/hmmer/hmmp… │ check_local_copy: Local copy │ +│ │ │ of module does not match │ +│ │ │ remote │ +│ hmmer/hmmsearch │ modules/nf-core/hmmer/hmms… │ check_local_copy: Local copy │ +│ │ │ of module does not match │ +│ │ │ remote │ +│ multiqc │ modules/nf-core/multiqc/ma… │ check_local_copy: Local copy │ +│ │ │ of module does not match │ +│ │ │ remote │ +│ ╵ ╵ │ +╰──────────────────────────────────────────────────────────────────────────────╯ + +╭─ [!] 18 Subworkflow Test Warnings ───────────────────────────────────────────╮ +│ ╷ ╷ │ +│ Subworkflow name │ File path │ Test message │ +│╶────────────────────────────────┼─────────────────────┼─────────────────────╴│ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'UTILS_NEXTFLOW_PIPE │ +│ │ │ LINE' versions are │ +│ │ │ not added in │ +│ │ │ main.nf. Can be │ +│ │ │ ignored if the │ +│ │ │ module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'UTILS_NFCORE_PIPELI │ +│ │ │ NE' versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'UTILS_NFVALIDATION_ │ +│ │ │ PLUGIN' versions are │ +│ │ │ not added in │ +│ │ │ main.nf. Can be │ +│ │ │ ignored if the │ +│ │ │ module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'completionEmail' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'completionSummary' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'dashedLine' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'fromSamplesheet' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'imNotification' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'nfCoreLogo' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'paramsSummaryMap' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ main_nf_include_vers │ +│ │ │ ions: Included │ +│ │ │ component │ +│ │ │ 'workflowCitation' │ +│ │ │ versions are not │ +│ │ │ added in main.nf. │ +│ │ │ Can be ignored if │ +│ │ │ the module is using │ +│ │ │ topic channels │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ meta_yml_exists: │ +│ │ │ Subworkflow meta.yml │ +│ │ │ does not exist │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ subworkflow_todo: │ +│ │ │ TODO string in │ +│ │ │ main.nf: Only │ +│ │ │ uncomment below if │ +│ │ │ logic in │ +│ │ │ toolCitationText/too │ +│ │ │ lBibliographyText │ +│ │ │ has been filled! │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ subworkflow_todo: │ +│ │ │ TODO string in │ +│ │ │ main.nf: Optionally │ +│ │ │ add bibliographic │ +│ │ │ entries to this │ +│ │ │ list. │ +│ utils_nfcore_nottocode_pipeline │ subworkflows/local… │ subworkflow_todo: │ +│ │ │ TODO string in │ +│ │ │ main.nf: Optionally │ +│ │ │ add in-text citation │ +│ │ │ tools to this list. │ +│ utils_nextflow_pipeline │ subworkflows/nf-co… │ subworkflow_version: │ +│ │ │ New version │ +│ │ │ available │ +│ utils_nfcore_pipeline │ subworkflows/nf-co… │ subworkflow_version: │ +│ │ │ New version │ +│ │ │ available │ +│ utils_nfvalidation_plugin │ subworkflows/nf-co… │ subworkflow_version: │ +│ │ │ New version │ +│ │ │ available │ +│ ╵ ╵ │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭───────────────────────╮ +│ LINT RESULTS SUMMARY │ +├───────────────────────┤ +│ [✔] 200 Tests Passed │ +│ [?] 3 Tests Ignored │ +│ [!] 47 Test Warnings │ +│ [✗] 29 Tests Failed │ +╰───────────────────────╯ diff --git a/nextflow.config b/nextflow.config index 7bed4e9..0ce0a7d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -84,19 +84,8 @@ params { // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -//try { -// includeConfig "${params.custom_config_base}/nfcore_custom.config" -//} catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -//} - -// Load nf-core/nottocode custom profiles from different institutions. -// -// includeConfig "${params.custom_config_base}/pipeline/nottocode.config" -//} catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/nottocode profiles: ${params.custom_config_base}/pipeline/nottocode.config") -//} +// Load nf-core custom profiles from different institutions +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" profiles { debug { dumpHashes = true diff --git a/nextflow_schema.json b/nextflow_schema.json index 6b00416..fa9fd1b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/nottocode/master/nextflow_schema.json", "title": "nf-core/nottocode pipeline parameters", "description": "lnc finder", @@ -292,5 +292,52 @@ { "$ref": "#/definitions/generic_options" } - ] + ], + "properties": { + "tpm_threshold": { + "type": "number", + "default": 0.1 + }, + "pfam_db": { + "type": "string" + }, + "multiqc_replace_names": { + "type": "string" + }, + "multiqc_sample_names": { + "type": "string" + }, + "mstrg_prep_script": { + "type": "string", + "default": "/home/gleison/Downloads/not2code_tests/not2code/assets/mstrg_prep.pl" + }, + "plek": { + "type": "string", + "default": "/home/gleison/Downloads/not2code_tests/not2code/assets/PLEK.1.2.tar.xz" + }, + "lncselect": { + "type": "string", + "default": "/home/gleison/Downloads/not2code_tests/not2code/assets/lncselect.R" + }, + "filter_by_tpm": { + "type": "boolean", + "default": true + }, + "reference_genome": { + "type": "string" + }, + "reference_gtf": { + "type": "string" + }, + "validationSkipDuplicateCheck": { + "type": "boolean", + "default": true + }, + "validationS3PathCheck": { + "type": "boolean" + }, + "monochromeLogs": { + "type": "boolean" + } + } } From 7cbcd2bb571819dc6c52dba0db30c6ed5847ae30 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Thu, 23 Apr 2026 15:46:52 -0300 Subject: [PATCH 12/13] update doc --- README.md | 70 ++++++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 62 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index ce9036f..b7a1dbe 100644 --- a/README.md +++ b/README.md @@ -87,27 +87,81 @@ graph TD > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +The `nf-core/nottocode` pipeline requires assembled transcriptomes (GTF files) as input. A typical workflow involves running `nf-core/rnaseq` first to align reads and assemble transcripts, followed by `nf-core/nottocode` to identify lncRNAs. -First, prepare a samplesheet with your input data that looks as follows: +### 1. Run nf-core/rnaseq -`samplesheet.csv`: +First, run `nf-core/rnaseq` with an aligner like HISAT2. You should also ensure StringTie is properly parameterized to preserve transcripts that are candidates for lncRNAs (e.g. modifying minimum junction coverage, minimum read coverage, and minimum length). + +Here is an example of creating a custom configuration for StringTie and running the `rnaseq` pipeline: + +```bash +# Create custom StringTie configuration +echo "process { + withName: 'NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE' { + ext.args = { + [ + '-j 3', + '-c 3', + '-m 200', + params.stringtie_extra_args ?: '' + ].join(' ').trim() + } + } +}" > stringtie.config + +# Run nf-core/rnaseq +nextflow run nf-core/rnaseq \ + -profile docker \ + -r 3.19.0 \ + --input rnaseq_samplesheet.csv \ + --outdir results_rnaseq \ + --fasta /path/to/genome.fna \ + --gtf /path/to/genome.gtf \ + --trimmer fastp \ + --aligner hisat2 \ + --skip_pseudo_alignment \ + -c stringtie.config +``` + +### 2. Prepare the input samplesheet + +After the `rnaseq` pipeline finishes, you need to prepare a samplesheet for `nottocode`. The samplesheet requires two columns: `sample` and `gtf`. You can create this automatically from the `rnaseq` StringTie outputs using the following bash script: + +```bash +# Output samplesheet file +output="gtf_samplesheet.csv" + +# Write header +echo "sample,gtf" > "$output" + +# List .transcripts.gtf files and process each one +for path in results_rnaseq/hisat2/stringtie/*transcripts.gtf; do + sample=$(basename "$path" .transcripts.gtf) + echo "$sample,$(realpath $path)" >> "$output" +done +``` + +This will create a `gtf_samplesheet.csv` that looks like this: ```csv sample,gtf -CONTROL_REP1,AEG588A1.gtf +CONTROL_REP1,/path/to/results_rnaseq/hisat2/stringtie/CONTROL_REP1.transcripts.gtf ``` -Each row represents a gtf file. +### 3. Run nf-core/nottocode -Now, you can run the pipeline using: +Now, you can run the `nottocode` pipeline using the generated samplesheet: ```bash nextflow run nf-core/nottocode \ - --input /path/to/samplesheet.csv \ - --reference_gtf /path/to/genome.gff \ + -profile docker \ + --input gtf_samplesheet.csv \ + --reference_gff /path/to/genome.gff \ + --reference_gtf /path/to/genome.gtf \ --reference_genome /path/to/genome.fna \ --pfam_db /path/to/Pfam-A.hmm \ - --outdir results + --outdir results_nottocode ``` From 936ecebc092699ee702e14870c2f858194a570d3 Mon Sep 17 00:00:00 2001 From: gleisonm Date: Thu, 23 Apr 2026 15:52:37 -0300 Subject: [PATCH 13/13] update doc --- README.md | 41 ++++++++++++++++------------------------- 1 file changed, 16 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index b7a1dbe..668ca1b 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,24 @@

- - nf-core/nottocode + + nf-core/not2code

-[![GitHub Actions CI Status](https://github.com/nf-core/nottocode/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/nottocode/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/nottocode/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/nottocode/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/nottocode/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/not2code/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/nottocode) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/not2code) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23nottocode-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/nottocode)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23not2code-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/not2code)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction -**nf-core/nottocode** is a bioinformatics designed to annotate long non-coding RNAs (lncRNAs) from transcriptome assemblies. It works by filtering, comparing, and characterizing transcripts from GTF files, which can be generated by tools such as stringtie via nf-core/rnaseq. +**not2code** is a bioinformatics pipeline designed to annotate long non-coding RNAs (lncRNAs) from transcriptome assemblies from small bulk RNA-seq data. It works by filtering, comparing, and characterizing transcripts from GTF files, which can be generated by tools such as StringTie via nf-core/rnaseq. The pipeline performs the following key steps: @@ -87,7 +86,7 @@ graph TD > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. -The `nf-core/nottocode` pipeline requires assembled transcriptomes (GTF files) as input. A typical workflow involves running `nf-core/rnaseq` first to align reads and assemble transcripts, followed by `nf-core/nottocode` to identify lncRNAs. +The `not2code` pipeline requires assembled transcriptomes (GTF files) as input. A typical workflow involves running `nf-core/rnaseq` first to align reads and assemble transcripts, followed by `dalmolingroup/not2code` to identify lncRNAs. ### 1. Run nf-core/rnaseq @@ -126,7 +125,7 @@ nextflow run nf-core/rnaseq \ ### 2. Prepare the input samplesheet -After the `rnaseq` pipeline finishes, you need to prepare a samplesheet for `nottocode`. The samplesheet requires two columns: `sample` and `gtf`. You can create this automatically from the `rnaseq` StringTie outputs using the following bash script: +After the `rnaseq` pipeline finishes, you need to prepare a samplesheet for `not2code`. The samplesheet requires two columns: `sample` and `gtf`. You can create this automatically from the `rnaseq` StringTie outputs using the following bash script: ```bash # Output samplesheet file @@ -149,25 +148,25 @@ sample,gtf CONTROL_REP1,/path/to/results_rnaseq/hisat2/stringtie/CONTROL_REP1.transcripts.gtf ``` -### 3. Run nf-core/nottocode +### 3. Run nf-core/not2code -Now, you can run the `nottocode` pipeline using the generated samplesheet: +Now, you can run the `not2code` pipeline using the generated samplesheet: ```bash -nextflow run nf-core/nottocode \ +nextflow run dalmolingroup/not2code \ -profile docker \ --input gtf_samplesheet.csv \ --reference_gff /path/to/genome.gff \ --reference_gtf /path/to/genome.gtf \ --reference_genome /path/to/genome.fna \ --pfam_db /path/to/Pfam-A.hmm \ - --outdir results_nottocode + --outdir results_not2code ``` ## Pipeline output -To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/nottocode/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/not2code/results) tab on the nf-core website pipeline page. The pipeline will create a simplified output structure under the designated `--outdir` parameter (e.g. `results/`): @@ -178,23 +177,15 @@ The pipeline will create a simplified output structure under the designated `--o * `pipeline_info/`: Generic logs and reports relating to the execution of the Nextflow pipeline. For more details about the output files and reports, please refer to the -[output documentation](https://nf-co.re/nottocode/output). +[output documentation](https://nf-co.re/not2code/output). ## Credits -nf-core/nottocode was developed by @gleisonm and @rafaellaferraz. - -We thank all contributors to the nf-core community for support and feedback. - -## Contributions and Support - -If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). - -For further information or help, don't hesitate to get in touch on the [Slack `#nottocode` channel](https://nfcore.slack.com/channels/nottocode) (you can join with [this invite](https://nf-co.re/join/slack)). +not2code was developed by @gleisonm and @rafaellaferraz. ## Citations -If you use nf-core/nottocode for your analysis, please cite it using its Digital Object Identifier (DOI). +If you use dalmolingroup/not2code for your analysis, please cite it using its Digital Object Identifier (DOI). An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.