Fix input channels for variantrecalibrator #1022
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Changelog :) |
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"Fix" doesn't work when either |
…_snps_vqsr and dbsnp_vqsr
…vqsr are channels and not strings
asp8200
commented
May 15, 2023
workflows/sarek.nf
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| dbsnp_vqsr = params.dbsnp_vqsr ?: Channel.empty() | ||
| known_indels_vqsr = params.known_indels_vqsr ?: Channel.empty() | ||
| known_snps_vqsr = params.known_snps_vqsr ?: Channel.empty() | ||
| dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() |
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@FriederikeHanssen and @maxulysse : The joint-germline genotyping now seems to work both when known_snps_vqsr etc. are set and when they are not.
Should we do a similar initialisation of the other channels in this section?
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Is there any way I could test the changes from this PR, to see if they solve #1016 ? |
maxulysse
approved these changes
May 16, 2023
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Yes, you can run: nextflow run asp8200/sarek -r fix_variantrecalibrator ... |
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that would be great @amizeranschi to test that it all works now :) |
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I tested this now and can confirm that this PR fixes #1016. |
Just need the changelog and we're good to go |
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Fix input channels for variantrecalibrator in the joint-germline workflow.
There is currently no pytest testing that this works. I tested it manually with downsampled versions of the giab-samples HG002 and HG003.
PR checklist
nf-core lint).nextflow run . -profile 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).