nf-core_modules/modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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New module: `metabat2` (#875) * 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 * compressing and removing not reproducible md5sums * follow symlinks while decompressing * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf 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> * Update modules/metabat2/metabat2/main.nf 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> * answer PR comments and switch to bgzip Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:08:26 +00:00
name: metabat2_jgisummarizebamcontigdepths
description: Depth computation per contig step of metabat2
keywords:
- sort
- binning
- depth
- bam
- coverage
- de novo assembly
tools:
- metabat2:
description: Metagenome binning
homepage: https://bitbucket.org/berkeleylab/metabat/src/master/
documentation: https://bitbucket.org/berkeleylab/metabat/src/master/
tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/
doi: "10.7717/peerj.7359"
licence: ['BSD-3-clause-LBNL']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Sorted BAM file of reads aligned on the assembled contigs
pattern: "*.bam"
- bai:
type: file
description: BAM index file
pattern: "*.bam.bai"
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"
- depth:
type: file
description: Text file listing the coverage per contig
pattern: ".txt.gz"
authors:
- "@maxibor"