mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
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
|
|
description: Reheader a VCF file
|
|
keywords:
|
|
- reheader
|
|
- vcf
|
|
- update header
|
|
tools:
|
|
- reheader:
|
|
description: |
|
|
Modify header of VCF/BCF files, change sample names.
|
|
homepage: http://samtools.github.io/bcftools/bcftools.html
|
|
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
|
|
doi: 10.1093/gigascience/giab008
|
|
licence: ['GPL']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- vcf:
|
|
type: file
|
|
description: VCF/BCF file
|
|
pattern: "*.{vcf.gz,vcf,bcf}"
|
|
- fai:
|
|
type: file
|
|
description: Fasta index to update header sequences with
|
|
pattern: "*.{fai}"
|
|
- header:
|
|
type: file
|
|
description: New header to add to the VCF
|
|
pattern: "*.{header.txt}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
- vcf:
|
|
type: file
|
|
description: VCF with updated header
|
|
pattern: "*.{vcf.gz}"
|
|
|
|
authors:
|
|
- "@bjohnnyd"
|