mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
ec15d0f9fd
* 📦 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>
67 lines
1.7 KiB
YAML
67 lines
1.7 KiB
YAML
name: pbccs
|
|
description: Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads
|
|
keywords:
|
|
- ccs
|
|
tools:
|
|
- pbccs:
|
|
description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
|
|
homepage: https://github.com/PacificBiosciences/pbbioconda
|
|
documentation: https://ccs.how/
|
|
tool_dev_url: https://github.com/PacificBiosciences/ccs
|
|
doi: ""
|
|
licence: ['BSD-3-Clause-Clear']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
id: id of the split file
|
|
- bam:
|
|
type: file
|
|
description: Raw subreads bam
|
|
pattern: "*.subreads.bam"
|
|
- pbi:
|
|
type: file
|
|
description: Pacbio BAM Index
|
|
pattern: "*.pbi"
|
|
- chunk_num:
|
|
-type: integer
|
|
-description: BAM part to process
|
|
- chunk_on:
|
|
-type: integer
|
|
-description: Total number of bam parts to process
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: CCS sequences in bam format
|
|
pattern: "*.bam"
|
|
- pbi:
|
|
type: file
|
|
description: PacBio Index of CCS sequences
|
|
pattern: "*.pbi"
|
|
- report_txt:
|
|
type: file
|
|
description: Summary of CCS in txt format
|
|
pattern: ".txt"
|
|
- report_json:
|
|
type: file
|
|
description: Summary of CCS in txt json
|
|
pattern: ".json"
|
|
- metrics:
|
|
type: file
|
|
description: Metrics about zmws
|
|
pattern: "*.json.gz"
|
|
|
|
authors:
|
|
- "@sguizard"
|