Harshil Patel
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7b3315591a
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Remove def software lines and emit versions channel as plural (#780)
* Remove def software line
* Replace version with versions in emit statement
* Fix default software names
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2021-10-01 14:04:56 +01:00 |
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Harshil Patel
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9c31cf1566
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Fix version commands: round 3 (#754)
* Fix version commands: round 3
* Fix seqkit/split2 modules
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2021-09-28 14:37:47 +01:00 |
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Harshil Patel
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43c2779258
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Fix version commands (#749)
* Fix version commands
* Fix version commands: again
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2021-09-27 22:10:37 +01:00 |
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Gregor Sturm
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906577873b
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Bulk update modules to use versions.yml (#739)
* New functions.nf
* Convert code to create versions.yml
* Update meta.yml
* update output channel
* Fix more meta.yml
* Manually update remaining modules
* remove superflous echo
* Fix misformatted meta.yml files
* Fix yaml, was list instead of dict
* fix version for bcftools
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-09-27 09:41:24 +01:00 |
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Mahesh Binzer-Panchal
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58134cb929
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Chromap Module (#659)
* Initialise chromap module
* Revert "Initialise chromap module"
This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.
* Remake chromap base files with new layout
* Copy chromap
* Copy index
* Add compression
* Update padding
* Update container
* Update chromap input test data
* Add chromap chromap tests
* Add padding
* Update comment
* update yaml file
* Remove TODOs
* Add fasta input to yaml
* Update YAML
* Remove comment, update container
* Remove comments
* Import Chromap index
* Update test.yml
* Fix read input
* Update test.yml
* Add bcftools/concat module. (#641)
* draft for bcftools modules [ci skip]
* initial test for bcftools concat
* Update the params for testing
* fix tests
* Accomodate code review [ci skip]
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update the meta file and open PR for review
* Update the keyword
* Update the tags for module [ci skip[
* add threads
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add module for dragonflye (#633)
* add module for dragonflye
* fix tests for dragonflye
* Update test.yml
* Update meta.yml
* Update main.nf
* Update main.nf
* Update modules/dragonflye/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* update typos. change quote from ' to ". (#652)
* Add bcftools/norm module (#655)
* Initial draft [ci skip]
* trigger first test
* update output file path
* Tests passing
* finishing touches for meta.yml and update checksum
* tweak checksum
* add threads to the module
* skip version info for matching test md5sum [ci skip]
* Add ref fasta and finalize the module
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Expansionhunter (#666)
Please enter the commit message for your changes. Lines starting
* adds expansionhunter module
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update test.yml (#668)
* Specify in guidelines one should split CPUs when module has n > 1 tool (#660)
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Describe CPU splitting
* Update README.md
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* More CPU examples
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Add dsh-bio export-segments module (#631)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* update: `BWA/ALN` (#653)
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate.
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Update seqwish reported version to match bioconda version. (#678)
* Bbmap index (#683)
BBMap index module
* Initialise chromap module
* Revert "Initialise chromap module"
This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.
* Remove unnecessary files
* Remove unnecessary files
* Update modules/chromap/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/chromap/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/chromap/chromap/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/modules/chromap/chromap/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/modules/chromap/chromap/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/modules/chromap/chromap/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/chromap/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove pytest_software.yml
* Apply suggestions from code review
Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-09-15 17:20:55 +01:00 |
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