Minor fixes#16
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Update main.nf
Update main.nf
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testing changes
ozlemmuslu
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ozlemmuslu
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Hi,
Many thanks for the pull request. I added my comments here. Let's minimize the changes in this pull request to nextflow updates and upgrading the individual submodules. The torch GPU/CPU issue will be solved separately and less platform dependent
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I will be updating the torch in this environment, so please remove this part from the PR
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I am adding CPU support back, so let's remove this as well, thanks!
| log.info "[INFO] Samplesheet validated" | ||
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| def sep = ch_samplesheet_file.name.endsWith('.tsv') ? '\t' : ',' | ||
| def sep = params.samplesheet.endsWith('.tsv') ? '\t' : ',' |
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here it seems the file extension is read from params.samplesheet, but the file that's being read is ch_samplesheet. This looks error-prone, please use the same file path for both.
Also overall, there are variable names like samplesheet, ch_samplesheet, samplesheet_ch. are these all referring to the same file? if so, we can use the same name, if not, let's use more descriptive names
| samplesheet_ch.map { path -> | ||
| def header = path.text.readLines()[0] | ||
| def cols = header.split(/,|\t/) // handle CSV or TSV | ||
| def sep = path.name.endsWith('.tsv') ? '\t' : ',' |
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the variable sep was computed before the function call, and can be passed as an argument to this function
| error "Samplesheet is missing required columns: ${missing.join(', ')}" | ||
| } | ||
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| // Optional: check BAM files exist |
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The existence of BAM paths is checked elsewhere already:
VariantMedium/bin/prepare_input_files.py
Line 19 in 42ff4d0
2 participants
Minor testing changes
closes #13