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nf-core_modules/tests/modules/dastool/scaffolds2bin/test.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 test_dastool_scaffolds2bin
Dastool update to allow non-gzipped inputs (#1458) * fix: remove left-over unnecessary code * Make gzipping optional for DAS_Tool scaffolds2bin * Add optional unzipping * Make gunzip optional for DAS_Tool scaffolds2bin * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/dastool/scaffolds2bin/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-03-28 14:29:46 +00:00
command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config
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
tags:
- dastool
- dastool/scaffolds2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
Dastool update to allow non-gzipped inputs (#1458) * fix: remove left-over unnecessary code * Make gzipping optional for DAS_Tool scaffolds2bin * Add optional unzipping * Make gunzip optional for DAS_Tool scaffolds2bin * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/dastool/scaffolds2bin/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-03-28 14:29:46 +00:00
- path: output/dastool/versions.yml
md5sum: d0831ed159eb5a1a1565d1d211012ad6
- name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped
command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config
tags:
- dastool
- dastool/scaffolds2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml
md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f
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