Use project name instead of multisample #264
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jemten
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| @@ -33,10 +33,10 @@ process { | |||
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| withName: '.*:STRUCTURAL_VARIANT_CALLING:SNIFFLES_MULTISAMPLE' { | |||
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| ext.prefix = 'multisample_sniffles' | |||
| ext.prefix = { "${meta.id}_sniffles" } | |||
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| // Check that there's no more than one project | ||
| // TODO: Try to do this in nf-schema |
Genmod seems to work fine with multiple families(Clinical-Genomics/genmod@e1c3981) from what I can see, as long as there is at least one affected individual. The main issue seems to be memory usage when VCFs becomes too big. If this is an issue, we could think about splitting the VCF and ranking per family, if there are multiple families per project (#276). |
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This PR adds a project column to the samplesheet, that multisample output files are grouped on.
This would have the benefit of being able to run a case (at CG) with one family, where
family_idis equal toproject, e.g:which would output one VCF file containing one family, named
slowsaluki_*.vcf.gz, together with single sample VCFs.projectwould be imitating case in raredisease, but named project to avoid confusion.At the same time you would be able to run a bigger project, where multiple families would be included within the same project, e.g:
which would output one VCF file containing multiple families, named
bigproject_*.vcf.gz, together with single sample VCFs.After discussing with Ram, an alternative solution would be to add a
--project_modeparameter, that could change the grouping of the output from project to family_id, havingprojectas an optional column in the samplesheet. But in my opinion that might be more complicated than the proposed solution. A third option would be to just add a--multisample_output_nameparameter that decides the output name, but I think we both agreed that this is better done in the samplesheet.Additionally, this PR also moves the PED creation into a process (like in raredisease) and closes #158, removes the
--extra_snfsparameter, and #48 would be closed in favour of this.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).