mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
b399f22af2
* add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * first cmseq commit * compressing and removing not reproducible md5sums * save intermediate work * follow symlinks while decompressing * add cmseq/polymut * add polymut * add extra test with optional input file * remove metabat2 * Update modules/cmseq/polymut/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix file extension * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add test without bam index * split tests in workflows * answer PR review * report version from variable Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
61 lines
1.5 KiB
YAML
61 lines
1.5 KiB
YAML
name: cmseq_polymut
|
|
description: Calculates polymorphic site rates over protein coding genes
|
|
keywords:
|
|
- polymut
|
|
- polymorphic
|
|
- mags
|
|
- assembly
|
|
- polymorphic sites
|
|
- estimation
|
|
- protein coding genes
|
|
- cmseq
|
|
- bam
|
|
- coverage
|
|
tools:
|
|
- cmseq:
|
|
description: Set of utilities on sequences and BAM files
|
|
homepage: https://github.com/SegataLab/cmseq
|
|
documentation: https://github.com/SegataLab/cmseq
|
|
tool_dev_url: https://github.com/SegataLab/cmseq
|
|
licence: ['MIT License']
|
|
|
|
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"
|
|
- bai:
|
|
type: file
|
|
description: BAM index file
|
|
pattern: "*.bai"
|
|
- gff:
|
|
type: file
|
|
description: GFF file used to extract protein-coding genes
|
|
pattern: "*.gff"
|
|
- fasta:
|
|
type: file
|
|
description: Optional fasta file to run on a subset of references in the BAM file.
|
|
pattern: .{fa,fasta,fas,fna}
|
|
|
|
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"
|
|
- polymut:
|
|
type: file
|
|
description: Polymut report in `.txt` format.
|
|
pattern: "*.txt"
|
|
|
|
authors:
|
|
- "@maxibor"
|