comms convert renames its mzML output files from the raw filename to sample_id when a sample sheet is available, and downstream stages (search, rescore) use that file root going forwards. However, lfq seems to expect the original filename. If sample_id is not identical to raw file stem, the file is silently dropped with only a debug/warn log ("No sample sheet entry for ..."), and comms lfq / comms pipeline proceeds without that sample.
comms convertrenames its mzML output files from the raw filename tosample_idwhen a sample sheet is available, and downstream stages (search,rescore) use that file root going forwards. However,lfqseems to expect the original filename. Ifsample_idis not identical to raw file stem, the file is silently dropped with only a debug/warn log ("No sample sheet entry for ..."), andcomms lfq/comms pipelineproceeds without that sample.