Vcf2cytosure #456
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Vcf2cytosure #456
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Lucpen
reviewed
Dec 18, 2023
nextflow_schema.json
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| }, | ||
| "vcf2cytosure_switch": { | ||
| "type": "boolean", | ||
| "description": "Turn on the vcf2cytosure subworkflow", | ||
| "fa_icon": "fas fa-toggle-on", | ||
| "help_text": "vcf2cytosure can generate CGH files from a structural variant VCF file that can be analysed in the CytoSure interpretation software. Cut offs for allele frequencies and bin sizes can be modified in the config file. Turned off by default." |
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Instead of switch, I would call it something along the lines of skip_vcf2cytosure and have it set to true by default, that way it would be similar to hoe the rest of the switches are build.
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I know what you mean, it would be great to keep the naming consistent in the pipeline. I had it exactly like you suggested at first but ran into issues with turning turning the sub-workflow on using the command line. Since the flag was set to true by default, giving the option --skip_vcf2cytosure will just skip it again.
I will try to find a solution
Co-authored-by: Lucía Peña-Pérez <lucia.pena.perez@scilifelab.se>
Lucpen
reviewed
Dec 20, 2023
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| withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' { | ||
| ext.args = { [ | ||
| meta.sex.equals('1') ? '--sex male' : '--sex female', |
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If meta.sex is set to anything else than 1 it will default to female. I believe that is the general default of the program.
jemten
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Dec 20, 2023
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| withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' { | ||
| ext.args = { [ | ||
| meta.sex.equals('1') ? '--sex male' : '--sex female', |
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If meta.sex is set to anything else than 1 it will default to female. I believe that is the general default of the program.
Lucpen
approved these changes
Dec 20, 2023
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vcf2cytosure is a tool to convert SV vcf:s to a format that can be loaded into the CytoSure interpretation software. This PR includes a subworkflow for that tool. Since the workflow and tool is fairly specific to our setup it is turned off by default. It is turned on by supplying the option
--vcf2cytosure_switchPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).