Issue 509 & 313#533
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FriederikeHanssen
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maxulysse
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Easy to do indeed.
Should we have some tests for that?
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Probably a good idea. Let me add some |
| test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai | ||
| test1,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai | ||
| test3,XX,0,sample3,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai | ||
| test3,XX,1,sample4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai |
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I used to make sure that sample3 is not run. I think I am missing a couple of check sthough
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So basically I justed wanted to make sure we can test all options of the channel magic, that is why two "pairs". Single-normal, single-tumor, and a paired one. Or do you think that is too extensive?
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Ooooh I see.
May I suggest an alternative solution, not sure if it'll work or not, but could be worth a try
Have 3 different samplesheets:
- single normal
- single tumor
- pair
That way we can use those in different tests.
but call it here in this case with --input samplesheet1.csv,samplesheet2.csv,samplesheet3.csv
I know it worked on local with previous sarek version, might be working here as well in this case
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otherwise, happy with this idea, that's good and smart
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you can stop looking, managed to run:
nextflow run . -profile test,docker --input "tests/csv/3.0/fastq_*.csv"
There's no , involved, just * so won't work on https path, just s3 + local
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hm, ok what works locally now is nextflow run main.nf -profile test,variantcalling_channels,docker --input tests/csv/3.0/recalibrated_{germline,tumoronly,somatic}.csv --tools strelka
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it think it is the if (params.input) csv_file = file(params.input) line and how this is expanded https://www.nextflow.io/docs/latest/script.html#files-and-i-o
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yes, we can use globs, so * or {}, I'd say probably ?, but not https definitively
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ah never mind actually doesn't run the processes except for the first file.
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ok one last thing, there is actually a |
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Closes #509
closes #313
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).