Issue 348 #419
Merged
Issue 348 #419
+530
−143
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fellen31
reviewed
Oct 8, 2024
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Cool! For some subworkflows, I've implemented subworkflow tests (#129). You can see that the CALL_SVS test is now failing, and you need to update the tests to reflect you now have 6 inputs instead of 5. Let me know if you need any help 😊
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The new linter in nf-core tools 3.0.0 complains about the schema's draft. Just seems to be the protocol (http vs https). Should I push the fix in this PR or do we go about this another way? |
I'll work on merging the 3.0.0 template PR later today. In the meantime, if the change required for it to work is only to change http to https, then you can fix that in this PR :) |
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I tried doing that but it continued to produce more errors. 😵💫 So I'll put this on hold and merge your changes into my branch when you're done |
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I rebased my branch onto dev without conflicts. So everything should be fine now 🤞 |
fellen31
approved these changes
Oct 10, 2024
| input[2] = SAMTOOLS_FAIDX.out.fai | ||
| input[3] = "sniffles" | ||
| input[4] = [[],[]] | ||
| input[5] = [ |
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I think this is okay (and I've done similarly), but I'm not sure the coordinates in this file will overlap with any variants we call in this test (?).
If you wanted to, you could check the variants output in this test without any bed file, and then choose an appropriate region overlapping a variant.
You can "create" a custom bed file like this:
https://github.com/nf-core/modules/blob/d7462e71f9129083ce10c3fe953ed401781e0ebd/modules/nf-core/modkit/pileup/tests/main.nf.test#L110-L112
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Also the |
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Closes #348. The input BED file is now passed through to CALL_SVS, which passes it to BEDTOOLS_MERGE for region-based filtering of SVs during merging.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).