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Sarek FASTQ samplesheets fail validation because BAM and BAI are always required #1297
Description
Summary
On main at 95bdacc803aa5cfdb10f35e5b9fb2d4b11100133, Sarek samplesheet generation reports missing BAM and BAI columns for FASTQ input.
Steps to reproduce
- Put two valid, paired gzip FASTQ files named
T1-X_R1_001.fastq.gzandT1-X_R2_001.fastq.gzin./fastqs. I used one record in each file:@read1,ACGT,+,!!!!. - From the repository root, run:
python bio-research/skills/nextflow-development/scripts/generate_samplesheet.py ./fastqs sarek --input-type fastq -o sarek.csvObserved behavior
The script finds and pairs both FASTQs into one row and infers tumor status 1, then reports:
Row 2: Missing required column 'bam'
Row 2: Missing required column 'bai'
Accepting the default N at Proceed anyway? exits 1 without writing a samplesheet. Adding --no-interactive prints the same errors, writes a sheet, and exits 0.
Expected behavior
A FASTQ row should not require BAM or BAI columns. The Sarek configuration applies those requirements only when the input type is BAM or CRAM.
Cause and verification
The validator collects every required column, then leaves the conditional check as pass. I reproduced the behavior on Windows with Python 3.14.8 using actual decompressible gzip FASTQs, in both interactive and noninteractive modes. I did not run the Nextflow pipeline.
Activity
mansi-singh4 commentedon Oct 11, 2026
Hi @agammann
if you are not already working on this issue i would like to take it up.
agammann commentedon Oct 11, 2026
Thanks—please feel free to take it up.
agammann commentedon Oct 13, 2026
A clarification to my earlier reply, @mansi-singh4: I reported the issue, and the maintainers handle upstream changes. The repo's external PR workflow is set up to close non-member PRs that change plugin code, so please check with a maintainer before investing time in a PR.
mansi-singh4 commentedon Oct 13, 2026
yeah that had occurred to me too... but I am new to open source and have no idea how to contact with the maintainers here...
agammann commentedon Oct 14, 2026
You can ask right here in this issue, @mansi-singh4. For example: "Could a maintainer advise whether an external fix for this bug would be welcome, and how I should submit it under the current PR policy?" Then give them time to respond before preparing a PR.