Gatkcnvcaller #362
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Gatkcnvcaller #362
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…redisease into gatkcnvcaller
…redisease into gatkcnvcaller
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jemten
approved these changes
Jul 7, 2023
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| withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WES' { | ||
| ext.args = { "--bin-length 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } |
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| ext.args = { "--bin-length 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } | |
| ext.args = { "--bin-length 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } |
| @@ -117,4 +117,15 @@ process { | |||
| enabled: false | |||
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| withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WGS' { | |||
| ext.args = { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } | |||
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| ext.args = { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } | |
| ext.args = { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" } |
docs/output.md
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| #### GATK GermlineCNVCaller (CNV calling) | ||
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| #### GATK GermlineCNVCaller (CNV calling) |
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| #!/usr/bin/env nextflow | |||
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Is it the new standard to add a shebang for nextflow subworkflows? We should add it to the subworkflows as well then (another PR).
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Nope.. removed it.
jemten
reviewed
Jul 7, 2023
| GATK4_COLLECTREADCOUNTS ( input, ch_fasta, ch_fai, ch_genome_dictionary ) | ||
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| GATK4_COLLECTREADCOUNTS.out.tsv | ||
| .groupTuple() |
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Its actually not necessary here.. I have removed it now.
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PR checklist
This PR adds GATK's germline CNV calling workflow to the pipeline, and includes relevant changes in the documentation.
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).