Gregor Sturm
ab67a1d41b
Update fastqc to produce multi-version versions.yml ( #665 )
...
* Update fastqc to produce multi-version versions.yml
* Update readme and pull request template
* Fix markdownlint
* remove variable
* Change publish dir to lowercase
* Re-add getSoftwareName
* Add custom pytest-workflow test to ensure versions.yml is valid
* Add docstring
* Remove __init__.py as it is not needed
* Remove changes to README, since this part went to nf-co.re
* Add NF_CORE_TEST env var
* Fix editorconfig
* Add additional consistency checks for versions.yml
* Update multiqc module
* Fix output channel
2021-09-24 10:01:54 +01:00
Sébastien Guizard
bbf268c5d3
new module: pbccs ( #688 )
...
* 📦 NEW: First commit of pbccs module
* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)
* 👌 IMPROVE: Move .pbi output into report channel
* 🐛 FIX: Correct code after --rq option removal from command line module
- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums
* 🐛 FIX: Repair additionnal option usage
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: CCS is run in parallel with --chunk option
* 👌 IMPROVE: Add Pbindex in bam ouput channel
* 👌 IMPROVE: Change label to process_low
* 👌 IMPROVE: Define reports files names + add json version of txt report
* 🐛 FIX: Add missing backslashes
* 🐛 FIX: Add missing gz extension
* 🐛 FIX: update ouput channel
* 🐛 FIX: output file name
* 👌 IMPROVE: .gitignore
* 👌 IMPROVE: Update function.nf to last version
* 👌 IMPROVE: Update saveAs in main.nf
* 👌 IMPROVE: Add pbccs module
* 🐛 FIX: Fix Broken test
* 👌 IMPROVE: Update test_data.config
* 🐛 FIX: Fix test
* 👌 IMPROVE: Update path of test dataset files
* 👌 IMPROVE: Remove useless index + Fix Typos
* 📦 NEW: First commit of pbccs module
* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)
* 👌 IMPROVE: Move .pbi output into report channel
* 🐛 FIX: Correct code after --rq option removal from command line module
- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums
* 🐛 FIX: Repair additionnal option usage
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: CCS is run in parallel with --chunk option
* 👌 IMPROVE: Add Pbindex in bam ouput channel
* 👌 IMPROVE: Change label to process_low
* 👌 IMPROVE: Define reports files names + add json version of txt report
* 🐛 FIX: Add missing backslashes
* 🐛 FIX: Add missing gz extension
* 🐛 FIX: update ouput channel
* 🐛 FIX: output file name
* 👌 IMPROVE: .gitignore
* 👌 IMPROVE: Update function.nf to last version
* 👌 IMPROVE: Update saveAs in main.nf
* 👌 IMPROVE: Add pbccs module
* 🐛 FIX: Fix Broken test
* 👌 IMPROVE: Update test_data.config
* 🐛 FIX: Fix test
* 👌 IMPROVE: Update path of test dataset files
* 👌 IMPROVE: Remove useless index + Fix Typos
* 🐛 FIX: fill contains args
* 👌 IMPROVE: One output => One Channel
* 👌 IMPROVE: One input => One channel
* 🐛 FIX: Update tests
* 🐛 FIX: Remove TODOs from test.yaml
* 👌 IMPROVE: Revert and keep bam and pbi together
* 🐛 FIX: Remove old rq input from meta.yml
* 👌 IMPROVE: Update test to match input channels
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 11:48:18 +01:00
Daniel Lundin
d7a3286a9a
New module to use hmmalign from HMMER to align sequences ( #470 )
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* Ignore vim tmp files
* Added hmmalign module, not yet tests
* Test output
* Replaced functions.nf for hmmalign with upstream
* Update software/hmmer/hmmalign/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/hmmer/hmmalign/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/hmmer/hmmalign/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/hmmer/hmmalign/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/hmmer/hmmalign/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/hmmer/hmmalign/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/hmmer/hmmalign/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-28 11:21:24 +01:00
Chris Cheshire
1aa7ed187a
seacr | Updated gitignore to ignore output folder
2020-12-17 14:23:07 +00:00
Gregor Sturm
f7c42ac4fd
Add tests for fastqc module
2020-07-15 09:48:14 +02:00
Gregor Sturm
4ee6ddc7ab
Update README
2020-07-14 10:55:38 +02:00
drpatelh
ef8c13a7d8
Fill out repo
2019-07-26 10:19:07 +01:00
