Sébastien Guizard
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8524e6b40f
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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>
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2021-10-23 19:09:41 +01:00 |
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