new module : jvarkit/vcffilterjdk #6621
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| def script_file = code?"--script \"${code}\"":"" | ||
| def regions_file = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":"" | ||
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| extension = getVcfExtension(args3); /* custom function, see below */ |
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I would not use a function here, just put it straight in
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@jfy133 this statement contradicts what I've been told here https://nfcore.slack.com/archives/CJRH30T6V/p1725629116371819
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grumble grumble @nvnieuwk have you being saying yes to others on this? I thought we were trying to avoid such complexity in modules as an approximate rule ?
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I thought it seemed reasonable 😁 I didn't know about us trying to avoid this, my bad. If that's the case than we shouldn't do this
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My philosphy if you do something more than two times then funciton it, otherwise it's adding more complexity. But #small-mound-i-feel-strongly-about-but-not-enough-to-fight-everyone
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That's what's happening here right? (sorry didn't take a closer look to it yet, it's a chaotic day) 😁
| Groovy Map containing code information | ||
| - code: | ||
| type: file | ||
| description: custom user Code . May be empty if script if provided via `task.ext.args2`. |
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| description: custom user Code . May be empty if script if provided via `task.ext.args2`. | |
| description: custom user code. May be empty if script if provided via `task.ext.args2`. |
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| process { | |||
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…nfcore-modules into pl_jvarkit_vcffilterjdk
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@jfy133 back to you. I added a test to check that a test with 'bed' is OK. Nevertheless Conda is failing "The operation was canceled." for an unknown reason. |
The conda error was just Azure saying nope, a restart seemed to have fixed it :) |
| e.g. [ id:'test_reference' ] | ||
| - fasta: | ||
| type: file | ||
| description: Groovy Map containing fasta reference genome information |
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You have not changed it since I first commented on this - does the tool expect multiple FASTA files?
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I'm not sure I understand the problem your comment here. No, there is only one fasta file. Where is the confusion here ?
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'Groovy Map containing' is what is confusing me, it's jut the file no?
| e.g. [ id:'test_reference' ] | ||
| - fai: | ||
| type: file | ||
| description: Groovy Map containing fasta index information |
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Same as above... should this be a map?
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... hum.. no, there is only one fai file (?..)
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert file(process.out.vcf[0][1]).exists() }, |
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Does .variantsMD5 not work here, like you did above?
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The BED provided in the test dataset does not overlap any variant. The output vcf is empty, When I test the variants md5, I then get an error md5sum for empty file
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| path(process.out.vcf[0][1]), |
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For stubs I believe you can just use
| path(process.out.vcf[0][1]), | |
| process.out, |
within the snapshot
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@jfy133 that didn't work, there is an error (snap) (I keep path(process.out.vcf[0][1]),)
| e.g. [ id:'test_reference' ] | ||
| - fasta: | ||
| type: file | ||
| description: Groovy Map containing fasta reference genome information |
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| description: Groovy Map containing fasta reference genome information | |
| description: File containing fasta reference genome information |
| e.g. [ id:'test_reference' ] | ||
| - fai: | ||
| type: file | ||
| description: Groovy Map containing fasta index information |
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| description: Groovy Map containing fasta index information | |
| description: File containing fasta index information |
| e.g. [ id:'test_reference' ] | ||
| - dict: | ||
| type: file | ||
| description: Groovy Map containing reference genome information for GATK sequence dictionary |
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| description: Groovy Map containing reference genome information for GATK sequence dictionary | |
| description: File containing reference genome information for GATK sequence dictionary |
| e.g. [ id:'test_reference' ] | ||
| - code: | ||
| type: file | ||
| description: custom user code . May be empty if script if provided via `task.ext.args2`. |
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| description: custom user code . May be empty if script if provided via `task.ext.args2`. | |
| description: File containing custom user code. May be empty if script if provided via `task.ext.args2`. |
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I kept that function There should be no new error now, but with the new version 3.0.0dev of nf-core-tools there is a new lint error. ( That is quite demoralizing, especially as this version is not available on conda and I cannot test/fix this locally) |
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OK this looks good to me now @lindenb thanks for the patience! I agree the failing linting is not nice, I've complained on your behalf. I will force merge :D |
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@jfy133 cool ! thanks ! |
* vcffilterdjdk * update params * update params * oppsss tag and TODO * target/region * answers to review * f...g space * fix conda problem https://nfcore.slack.com/archives/CJRH30T6V/p1726233311260959 * add test+bed * reset polyx * prevent test exception md5sum for empty file * update main.nf.test * update meta.yml * remove suggestion --------- Co-authored-by: James A. Fellows Yates <[email protected]>
This module implements jvarkt/vcffilterjdk https://pubmed.ncbi.nlm.nih.gov/29186339/ which filters VCF files using a java expression compiled at runtime. eg:
PR checklist
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda