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Merged
schristley merged 4 commits into from
Sep 21, 2026
Merged

develop #31

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72daaea
update igblast
schristley Sep 14, 2026
89f0b1e
mapping for single FASTQ files
schristley Sep 18, 2026
0f893c1
new app versions
schristley Sep 21, 2026
307725b
new version
schristley Sep 21, 2026
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14 changes: 7 additions & 7 deletions app/scripts/config/AnalysisConfig.js
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ var AnalysisConfig = {
"vdjserver:activity:uses": {
"JobFiles": [ 'archive' ],
"SequenceFASTQ": [ 'sequence_reads', 'sequence_single_read', 'sequence_quality' ],
"SequenceFASTA": [ 'sequence_reads', 'sequence_single_read' ],
"SequenceFASTA": [ 'sequence_reads' ],
"SequenceQualityFiles": [ 'sequence_quality'],
"SequenceForwardPairedFiles": ['sequence_forward_paired_reads'],
"SequenceReversePairedFiles": ['sequence_reverse_paired_reads'] ,
Expand All @@ -115,9 +115,9 @@ var AnalysisConfig = {
"igblast": {
"vdjserver:name":"IgBlast",
"activity": {
"igblast-ls6-0.10": {
"igblast-ls6-0.11": {
"vdjserver:app:name": "igblast-ls6",
"vdjserver:app:version": "0.10",
"vdjserver:app:version": "0.11",
"vdjserver:app:default": true
}
},
Expand Down Expand Up @@ -169,9 +169,9 @@ var AnalysisConfig = {
"repcalc": {
"vdjserver:name":"RepCalc",
"activity": {
"repcalc2-ls6-0.9": {
"repcalc2-ls6-0.10": {
"vdjserver:app:name": "repcalc2-ls6",
"vdjserver:app:version": "0.9",
"vdjserver:app:version": "0.10",
"vdjserver:app:default": true
}
},
Expand Down Expand Up @@ -204,9 +204,9 @@ var AnalysisConfig = {
"cellranger": {
"vdjserver:name":"Cell Ranger",
"activity": {
"cellranger-ls6-10.0.0": {
"cellranger-ls6-0.2": {
"vdjserver:app:name": "cellranger-ls6",
"vdjserver:app:version": "10.0.0",
"vdjserver:app:version": "0.2",
"vdjserver:app:default": true
}
},
Expand Down
22 changes: 20 additions & 2 deletions app/scripts/models/AnalysisDocument.js
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Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,25 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata)
let use_type = app['vdjserver:activity:uses'][input_name][ut];
console.log(input_name, use_type);
switch(use_type) {
case 'sequence_single_read':
for (let i in rep['sample']) {
let seqfiles = rep['sample'][i]['sequencing_files'];
//console.log(seqfiles);
if (seqfiles['filename'] && seqfiles['file_type'] == 'fastq') {
found = true;
new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']);
let extra = {};
extra[input_name] = seqfiles['filename'];
extra['airr:Repertoire'] = rep['repertoire_id']
new_uses_id.push('vdjserver:app:inputs:' + activity_id + ':' + seqfiles['filename']);
if (project_file_map[seqfiles['filename']]) {
extra['vdjserver:uuid'] = project_file_map[seqfiles['filename']];
}
extras.push(extra);
}
}
break;

case 'sequence_forward_paired_reads':
// identifiers use the forward read file
for (let i in rep['sample']) {
Expand Down Expand Up @@ -225,7 +244,7 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata)
case 'sequence':
for (let i in rep['sample']) {
let seqfiles = rep['sample'][i]['sequencing_files'];
console.log(seqfiles);
//console.log(seqfiles);
if (seqfiles['filename'] && seqfiles['file_type'] == 'fasta') {
found = true;
new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']);
Expand All @@ -241,7 +260,6 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata)
}
break;

case 'sequence_single_read':
case 'sequence_quality':
case 'sequence_reads':
case 'archive':
Expand Down
2 changes: 1 addition & 1 deletion app/vdjserver-schema
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Submodule vdjserver-schema updated 1 files
+3 −10 vdjserver-schema.yaml
2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "vdjserver-api",
"version": "2.13.1",
"version": "2.14.0",
"description": "VDJServer Web Services",
"author": [
{
Expand Down