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fix txp2gene retrieval bug when salmon_index is supplied #202

Merged
merged 5 commits into from Mar 5, 2023
Merged

fix txp2gene retrieval bug when salmon_index is supplied #202

merged 5 commits into from Mar 5, 2023

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azedinez
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@azedinez azedinez commented Mar 1, 2023 •
edited

txp2gene is generated as part of the salmon indexing, but if an index is supplied, the file must be supplied manually

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
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@azedinez
require txp2gene file when a salmon_index supplied
da34f07 
txp2gene is generated as part of the salmon indexing, but if an index is supplied, the file must be supplied manually
@azedinez
modify assertion error to reflect changes
b0f8c84
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github-actions bot commented Mar 1, 2023 •
edited

nf-core lint overall result: Passed ✅

Posted for pipeline commit 73cb4b5

+| ✅ 158 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-01 17:56:02

pinin4fjords
pinin4fjords reviewed Mar 1, 2023
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subworkflows/local/alevin.nf Outdated
@@ -31,9 +31,9 @@ workflow SCRNASEQ_ALEVIN {
"""Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf'), or a genome fasta file
and a transcriptome fasta file ('--transcript_fasta`) if no index is given!""".stripIndent()

if (transcript_fasta) {
if (transcript_fasta || salmon_index) {
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Actually, maybe it would be neater if this whole conditional was deleted, and this was just part of the assertions above?

assert (salmon_index && txp2gene) || (genome_fasta && gtf) || (genome_fasta && transcript_fasta && txp2gene):
        """Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf'), or a genome fasta file
        and a transcriptome fasta file ('--transcript_fasta`) if no index and txp2gene is given!""".stripIndent()

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I agree! Done.

@azedinez
tidying up the assertion
1d1a0d8 
merging the conditional with the assertion on line 30
@azedinez
fix ci issue
5182197
@azedinez
fix ci syntax issue
73cb4b5
@grst grst merged commit a421066 into nf-core:dev Mar 5, 2023
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@pinin4fjords pinin4fjords pinin4fjords left review comments

@apeltzer apeltzer apeltzer approved these changes

@fmalmeida fmalmeida Awaiting requested review from fmalmeida

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4 participants
@azedinez @apeltzer @pinin4fjords @grst