Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config ( #1279 )
...
* 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
Sébastien Guizard
ec15d0f9fd
Update module: pbccs ( #1018 )
...
* 📦 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
* 👌 IMPROVE: use prefix for for output file name
* 👌 IMPROVE: Update to new versions.yml
* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2
* 👌 IMPROVE: Keep track of the former sample id in meta
* Update modules/pbccs/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: remove former_id from meta
* 👌 IMPROVE: Use chunk number in output filename
* 🐛 FIX: Update meta.yml
* 🐛 FIX: Update reports filenames with chunk number.
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:19:26 +00:00
Sébastien Guizard
8524e6b40f
Update of pbccs ( #835 )
...
* 📦 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
* 👌 IMPROVE: use prefix for for output file name
* 👌 IMPROVE: Update to new versions.yml
* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2
* 👌 IMPROVE: Keep track of the former sample id in meta
* Update modules/pbccs/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: remove former_id from meta
* 👌 IMPROVE: Use chunk number in output filename
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:09:41 +01:00
Kevin
3aacd46da2
Backfill software licenses meta ( #876 )
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* backfilled modules with meta.yml that had no license identifier
* harmonized BSD license names
* whitespace linting at modules/unzip/meta.yml:12
* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'
* Update modules/bcftools/index/meta.yml
`bcftools` is dual-licensed, use associative array to allow for multiple licenses
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
2021-10-22 15:39:54 -07:00
Harshil Patel
49da864287
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
Gregor Sturm
906577873b
Bulk update modules to use versions.yml ( #739 )
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* 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>
2021-09-27 09:41:24 +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
