mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
a21cc95c69
* template created for variantbam (#616) * Add bcftools reheader (#585) (#608) * 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> * fixed autogenerated biocontainter links * variantbam module passing all tests/lints (#616) * Added an optional output junction channel in STAR (#621) * Added an optional output channel for chimeric junctions * Fix in test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * removed qcreport output fixes #616 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>
46 lines
1.2 KiB
YAML
46 lines
1.2 KiB
YAML
name: variantbam
|
|
description: Filtering, downsampling and profiling alignments in BAM/CRAM formats
|
|
keywords:
|
|
- filter
|
|
- bam
|
|
- subsample
|
|
- downsample
|
|
- downsample bam
|
|
- subsample bam
|
|
tools:
|
|
- variantbam:
|
|
description: Filtering and profiling of next-generational sequencing data using region-specific rules
|
|
homepage: https://github.com/walaj/VariantBam
|
|
documentation: https://github.com/walaj/VariantBam#table-of-contents
|
|
tool_dev_url: https://github.com/walaj/VariantBam
|
|
doi: 10.1093/bioinformatics/btw111
|
|
licence: ['Apache2']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM/CRAM file
|
|
pattern: "*.{bam,cram}"
|
|
|
|
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}"
|
|
- bam:
|
|
type: file
|
|
description: Filtered or downsampled BAM file
|
|
pattern: "*.{bam}"
|
|
|
|
authors:
|
|
- "@bjohnnyd"
|