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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>
This commit is contained in:
Sébastien Guizard
GitHub
parent
3b600af50e
commit
ec15d0f9fd
4 changed files with 27 additions and 11 deletions
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@ -37,9 +37,9 @@ process PBCCS {
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ccs \\
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$bam \\
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${prefix}.chunk${chunk_num}.bam \\
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--report-file ${prefix}.report.txt \\
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--report-json ${prefix}.report.json \\
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--metrics-json ${prefix}.metrics.json.gz \\
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--report-file ${prefix}.chunk${chunk_num}.report.txt \\
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--report-json ${prefix}.chunk${chunk_num}.report.json \\
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--metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\
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--chunk $chunk_num/$chunk_on \\
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-j $task.cpus \\
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$options.args
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@ -42,10 +42,26 @@ output:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- css:
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- bam:
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type: file
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description: Consensus sequences
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pattern: "*.ccs.bam"
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description: CCS sequences in bam format
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pattern: "*.bam"
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- pbi:
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type: file
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description: PacBio Index of CCS sequences
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pattern: "*.pbi"
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- report_txt:
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type: file
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description: Summary of CCS in txt format
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pattern: ".txt"
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- report_json:
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type: file
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description: Summary of CCS in txt json
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pattern: ".json"
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- metrics:
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type: file
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description: Metrics about zmws
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pattern: "*.json.gz"
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authors:
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- "@sguizard"
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BIN
tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc
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BIN
tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc
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Binary file not shown.
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@ -4,12 +4,12 @@
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- pbccs
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files:
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- path: output/pbccs/alz.chunk2.bam
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md5sum: d1a0266d5df64b74409a21981071a1c6
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md5sum: 2b6451f2d0454eb08359cb84e2e4069c
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- path: output/pbccs/alz.chunk2.bam.pbi
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md5sum: 582a4500ddcb3f4a24a443192620d039
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- path: output/pbccs/alz.metrics.json.gz
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md5sum: 3112cda9744e3facbf38245d41aaf080
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- path: output/pbccs/alz.chunk2.metrics.json.gz
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contains: [ 'zmws' ]
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- path: output/pbccs/alz.report.json
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- path: output/pbccs/alz.chunk2.report.json
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contains: [ 'Created by pbcopper' ]
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- path: output/pbccs/alz.report.txt
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- path: output/pbccs/alz.chunk2.report.txt
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md5sum: bbc5bd7a1269345cf7a7f3d4c746024b
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