mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
632587a7fc
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add bamUtil trimBam * Update modules/bamutil/trimbam/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bamutil/trimbam/main.nf * Changes after code-review * YAML lint Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
51 lines
1.5 KiB
YAML
51 lines
1.5 KiB
YAML
name: bamutil_trimbam
|
||
description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
|
||
keywords:
|
||
- bam
|
||
- trim
|
||
- clipping
|
||
- bamUtil
|
||
- trimBam
|
||
tools:
|
||
- bamutil:
|
||
description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
|
||
homepage: https://genome.sph.umich.edu/wiki/BamUtil
|
||
documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
|
||
tool_dev_url: https://github.com/statgen/bamUtil
|
||
doi: "10.1101/gr.176552.114"
|
||
licence: ['GPL v3']
|
||
|
||
input:
|
||
- meta:
|
||
type: map
|
||
description: |
|
||
Groovy Map containing sample information
|
||
e.g. [ id:'test', single_end:false ]
|
||
- bam:
|
||
type: file
|
||
description: BAM file
|
||
pattern: "*.bam"
|
||
- trim_left:
|
||
type: integer
|
||
description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
|
||
- trim_right:
|
||
type: integer
|
||
description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
|
||
|
||
output:
|
||
- meta:
|
||
type: map
|
||
description: |
|
||
Groovy Map containing sample information
|
||
e.g. [ id:'test', single_end:false ]
|
||
- versions:
|
||
type: file
|
||
description: File containing software versions
|
||
pattern: "versions.yml"
|
||
- bam:
|
||
type: file
|
||
description: Trimmed but unsorted BAM file
|
||
pattern: "*.bam"
|
||
|
||
authors:
|
||
- "@jfy133"
|