nf-core_modules/modules/dastool/scaffolds2bin/meta.yml

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Add new module: Das Tool (#1004) * 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 * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * 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 * remove metabat2 from PR * fix linting errors * remove traling whitespace * 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 * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review 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>
2021-11-19 07:33:29 +00:00
name: dastool_scaffolds2bin
description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
keywords:
- binning
- das tool
- table
- de novo
- bins
- contigs
- assembly
- das_tool
tools:
- dastool:
description: |
DAS Tool is an automated method that integrates the results
of a flexible number of binning algorithms to calculate an optimized, non-redundant
set of bins from a single assembly.
homepage: https://github.com/cmks/DAS_Tool
documentation: https://github.com/cmks/DAS_Tool
tool_dev_url: https://github.com/cmks/DAS_Tool
doi: "10.1038/s41564-018-0171-1"
licence: ["BSD"]
Add new module: Das Tool (#1004) * 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 * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * 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 * remove metabat2 from PR * fix linting errors * remove traling whitespace * 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 * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review 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>
2021-11-19 07:33:29 +00:00
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins
pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
Add new module: Das Tool (#1004) * 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 * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * 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 * remove metabat2 from PR * fix linting errors * remove traling whitespace * 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 * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review 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>
2021-11-19 07:33:29 +00:00
- extension:
type: val
description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input.
Add new module: Das Tool (#1004) * 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 * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * 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 * remove metabat2 from PR * fix linting errors * remove traling whitespace * 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 * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review 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>
2021-11-19 07:33:29 +00:00
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"
- scaffolds2bin:
type: file
description: tabular scaffolds2bin file for DAS tool input
pattern: "*.scaffolds2bin.tsv"
authors:
- "@maxibor"