mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
added meta.yml for umitools (#860)
* added meta.yml for umitools * Update modules/umitools/dedup/meta.yml type: list --> type: file Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/umitools/dedup/meta.yml aww thanks @drpateh :D Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/umitools/dedup/meta.yml module can only handle one BAM at a time, ergo BAM files --> BAM file Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update meta.yml added `pattern` for input `bam` and `bai` * removed trailing whitespace to appease linter * added license to new meta.yml files * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
parent
3aacd46da2
commit
81ed0e0ff2
2 changed files with 93 additions and 0 deletions
47
modules/umitools/dedup/meta.yml
Normal file
47
modules/umitools/dedup/meta.yml
Normal file
|
@ -0,0 +1,47 @@
|
||||||
|
name: umitools_dedup
|
||||||
|
description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
|
||||||
|
keywords:
|
||||||
|
- umitools
|
||||||
|
- deduplication
|
||||||
|
tools:
|
||||||
|
- umi_tools:
|
||||||
|
description: >
|
||||||
|
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
|
||||||
|
and single cell RNA-Seq cell barcodes
|
||||||
|
documentation: https://umi-tools.readthedocs.io/en/latest/
|
||||||
|
license: ['MIT']
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- bam:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
BAM file containing reads to be deduplicated via UMIs.
|
||||||
|
pattern: "*.{bam}"
|
||||||
|
- bai:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
BAM index files corresponding to the input BAM file.
|
||||||
|
pattern: "*.{bai}"
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- bam:
|
||||||
|
type: file
|
||||||
|
description: BAM file with deduplicated UMIs.
|
||||||
|
pattern: "*.{bam}"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@drpatelh"
|
||||||
|
- "@grst"
|
||||||
|
- "@klkeys"
|
46
modules/umitools/extract/meta.yml
Normal file
46
modules/umitools/extract/meta.yml
Normal file
|
@ -0,0 +1,46 @@
|
||||||
|
name: umitools_extract
|
||||||
|
description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
|
||||||
|
keywords:
|
||||||
|
- umitools
|
||||||
|
- extract
|
||||||
|
tools:
|
||||||
|
- umi_tools:
|
||||||
|
description: >
|
||||||
|
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
|
||||||
|
and single cell RNA-Seq cell barcodes
|
||||||
|
documentation: https://umi-tools.readthedocs.io/en/latest/
|
||||||
|
license: ['MIT']
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- reads:
|
||||||
|
type: list
|
||||||
|
description: |
|
||||||
|
List of input FASTQ files whose UMIs will be extracted.
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- reads:
|
||||||
|
type: file
|
||||||
|
description: Extracted FASTQ files. |
|
||||||
|
For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
|
||||||
|
For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
|
||||||
|
pattern: "*.{fastq.gz}"
|
||||||
|
- log:
|
||||||
|
type: file
|
||||||
|
description: Logfile for umi_tools
|
||||||
|
pattern: "*.{log}"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@drpatelh"
|
||||||
|
- "@grst"
|
Loading…
Reference in a new issue