James A. Fellows Yates
03de60e6fa
Add CHECKM/QA ( #2137 )
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* Bump checkM version and add support for pre-defined database
* Add markfile output to checkm/lineagewf and add checkm/qa
* Remove unnecessary BAM from tests
* Fix channels to ensure single meta
* Blah
* Use secondary name evwyhere
* Remove second incovcatiojn
* Don't run module directrly for join
* And for the other test
* Correct module name
* Fix name again
* Try and fix out_format 9 not being picked up
* Contains to matches to allow regex
* Fix tests (finally)
* Fix verisoning
* [automated] Fix linting with Prettier
* Update modules/checkm/qa/main.nf
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-30 15:50:47 +02:00
James A. Fellows Yates
0ab15c5ee9
Update checkM version and add support for pre-defined database ( #2125 )
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Bump checkM version and add support for pre-defined database
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-28 14:48:18 +02:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config ( #1279 )
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* fix yml formatting
* allow fastq.gz and fq.gz as file input, add meta.yml and test
* fix yaml files
* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"
This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.
* prettier magic!
* fix comments for yamllint
* remove node version number
* fix linting errors
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
James A. Fellows Yates
a740a6ff48
New module: checkm/lineagewf ( #899 )
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* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Added but test failing due to null on output channel
* fix prefix variable
* Complete checkm_lineagewf
* Remove TODOs
* Add description of fasta_ext parameter
* Improve meta map for this context
* Update meta.yml
* Update modules/checkm/lineagewf/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 21:54:10 +01:00
