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a813e2e3a6
* local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
51 lines
1.2 KiB
YAML
51 lines
1.2 KiB
YAML
name: bcftools_reheader
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description: Reheader a VCF file
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keywords:
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- reheader
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- vcf
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- update header
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tools:
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- reheader:
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description: |
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Modify header of VCF/BCF files, change sample names.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
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doi: 10.1093/gigascience/giab008
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licence: ['GPL']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: VCF/BCF file
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pattern: "*.{vcf.gz,vcf,bcf}"
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- fai:
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type: file
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description: Fasta index to update header sequences with
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pattern: "*.{fai}"
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- header:
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type: file
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description: New header to add to the VCF
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pattern: "*.{header.txt}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- vcf:
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type: file
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description: VCF with updated header
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pattern: "*.{vcf.gz}"
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authors:
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- "@bjohnnyd"
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