Refactor mitochondrial analysis workflow #419
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Lucpen
reviewed
Sep 5, 2023
docs/usage.md
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| 5. Variant calling - Structural variants (SV) (Tiddit & Manta) | ||
| 6. SNV annotation & ranking (rohcall, vcfanno, ensembl VEP, GENMOD) | ||
| 7. SV annotation & ranking (SVDB query, ensembl VEP, GENMOD) | ||
| 8. Mitochondrial analysis | ||
| 8. Mitochondrial annotation | ||
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Mitochondrial annotation is 8 here, but was 9 before (line 23) and is 9 later on (line 245), check if it's correct
jemten
reviewed
Sep 5, 2023
| .genotyped_intervals_vcf | ||
| .collect{it[1]} | ||
| .set { gcnvcaller_vcf } | ||
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| CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta) | ||
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| // CALL_SV_MT_SHIFT (ch_mtshift_bam_bai, ch_mtshift_fasta) |
| @@ -0,0 +1,111 @@ | |||
| // | |||
| // Merge and annotate MT | |||
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Suggested change
| // Merge and annotate MT | |
| // Merge MT variants |
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| ch_mt_vcf | ||
| .combine(ANNOTATE_CADD.out.vcf.ifEmpty("null")) | ||
| .branch { it -> | ||
| merged: it[2].equals("null") | ||
| return [it[0], it[1]] | ||
| cadd: !(it[2].equals("null")) | ||
| return [it[2], it[3]] | ||
| } | ||
| .set { ch_for_mix } | ||
| ch_vep_in = ch_for_mix.merged.mix(ch_for_mix.cadd) |
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Is there reason to use the same type of channel combinations as in #421 ?
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
…ip ci] Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
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PR checklist
This PR,
skip_mt_analysiswhich was used to turn on/off the mitochondrial workflowskip_mt_annotationwhich can be used to turn on/off annotation and ranking for mitochondrial SNVsWith changes in this PR, mitochondrial SNVs will no longer be called by deepvariant, and they will come from the GATKs best practices workflow for mitochondria.
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).