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Add samtools cramsize #5743
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Add samtools cramsize #5743
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Adding name of the tool Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
Adding prefix to make the module set up more flexible. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
Changing `.baseName` by `prefix` in output names. Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
- Stub section added to main.nf script. - test.yml file added to module samtools/cramsize
* Update manta somatic * Update manta tumoronly
* add call subcommand * at calls runs now [skip ci] * add test files * linting * fix tests * add contains check * Update tests/modules/nf-core/varlociraptor/callvariants/main.nf Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]>
* add module template * first version * update testing and linting * update file naming * update test * fix test
* ngmerge first commit * main module code * complete module * remove trailing whitespace * fix versions.yml * fix version yml * versions yml * vyml * try vyml again * touch versions yml * vyml
* initial commit * module version 1 * full testing * linting * fix version yaml * fix version yaml command * fix version yml maybe this time please * fix version yml for real this time * try again versions yaml * fix version yml * vyml * version yaml * vyml * update ref to have meta
Co-authored-by: Steven Strong <[email protected]>
Fix metaeuk and add tests
* add -f option * update tests
* new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * update vardictjava
* Start adding modules from #scrnaseq for simpleaf * Fix tests * t2gene is necessary, simplify tests * Linteing fixes * Fix test files * Test fixes * prettier * Address feedback * Update test string- logs in newer version lack some messages * Apply suggestions from code review Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Post-review index fixes * Post-review quant fixes * add stubs * Add metas, fix meta usage * Appease eclint --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
module currently fails, i've fixed the error in icount-mini so now by bumping the version here we fix the issue (old matplotlib syntax)
* Set up nf-core template for purecn/run module * Add run script and I/O * Clean TODOs and set main script * Fix duplicate entry * Set up main script * [ci skip] Format with prettier * [ci skip] Address review question and set up stub * [ci skip] Set stub for testing * Reformat with prettier * [CI skip] Adjust some typos * [CI skip] Set up test script using stub * Set up test yml * Reformat with prettier * Set up meta.yml file and fix typos * Reformat with prettier * Fix typo * Remove quay.io from container string * Remove optional input argument * Add optional outputs and clean non-mandatory parameters * Clean non-mandatory outputs * Reformat outputs * Fix minor and address reviews
* new module: samtools/import * fix versions * fix versions some more * Update modules/nf-core/samtools/import/main.nf * fix meta
* Adding seqkit sliding command * Linting fix * Updating for better matching * reverted to regex using end line markers for better matching other wise fastq gets caught by fa, error in other modules * Added a test for fastq too --------- Co-authored-by: Matthieu Muffato <[email protected]>
* create module hicpca * Update modules/nf-core/hicexplorer/hicpca/main.nf Co-authored-by: Sébastien Guizard <[email protected]> * Update modules/nf-core/hicexplorer/hicpca/main.nf Co-authored-by: Sébastien Guizard <[email protected]> * add more keywords. * remove quay.io. --------- Co-authored-by: Sébastien Guizard <[email protected]>
Add "--force" to pigz
Splitting off the samtools cram-size from #3555 |
CarsonJM
approved these changes
Jun 3, 2024
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LGTM! Just a teeny change regarding how the test data path is specified.
Co-authored-by: Carson J Miller <[email protected]>
Co-authored-by: Carson J Miller <[email protected]>
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PR checklist
Closes #XXX
versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda