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Update of pbccs (#835)

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* 📦 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>
This commit is contained in:
Sébastien Guizard 2021-10-23 19:09:41 +01:00 committed by GitHub
parent d3369789da
commit 8524e6b40f
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
5 changed files with 26 additions and 29 deletions
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31
modules/pbccs/main.nf
View file

@ -11,11 +11,11 @@ process PBCCS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pbccs=6.0.0" : null)
conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pbccs:6.0.0--h9ee0642_2"
container "https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0"
} else {
container "quay.io/biocontainers/pbccs:6.0.0--h9ee0642_2"
container "quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0"
}
input:
@ -24,25 +24,22 @@ process PBCCS {
val chunk_on
output:
tuple val(meta), path("*.ccs.bam") , emit: bam
tuple val(meta), path("*.ccs.bam.pbi") , emit: pbi
tuple val(meta), path("*.ccs_report.txt" ) , emit: ccs_report_txt
tuple val(meta), path("*.ccs_report.json" ) , emit: ccs_report_json
tuple val(meta), path("*.zmw_metrics.json.gz"), emit: zmw_metrics
path "versions.yml" , emit: versions
tuple val(meta), path("*.chunk*.bam") , emit: bam
tuple val(meta), path("*.chunk*.bam.pbi") , emit: pbi
tuple val(meta), path("*.report.txt" ) , emit: report_txt
tuple val(meta), path("*.report.json" ) , emit: report_json
tuple val(meta), path("*.metrics.json.gz"), emit: metrics
path "versions.yml" , emit: versions
script:
def ccs = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs.bam'
def report_txt = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.txt'
def report_json = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.json'
def zmw_metrics = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.zmw_metrics.json.gz'
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
ccs \\
$bam \\
$ccs \\
--report-file $report_txt \\
--report-json $report_json \\
--metrics-json $zmw_metrics \\
${prefix}.chunk${chunk_num}.bam \\
--report-file ${prefix}.report.txt \\
--report-json ${prefix}.report.json \\
--metrics-json ${prefix}.metrics.json.gz \\
--chunk $chunk_num/$chunk_on \\
-j $task.cpus \\
$options.args

2
modules/pbccs/meta.yml
View file

@ -16,7 +16,7 @@ input:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
id: id of the split file
- bam:
type: file
description: Raw subreads bam

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tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc Normal file
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2
tests/modules/pbccs/main.nf
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@ -7,7 +7,7 @@ include { PBCCS } from '../../../modules/pbccs/main.nf' addParams( options: [arg
workflow test_pbccs {
input = [
[ id:'test' ], // meta map
[ id:'alz' ], // meta map
file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
]

20
tests/modules/pbccs/test.yml
View file

@ -3,13 +3,13 @@
tags:
- pbccs
files:
- path: output/pbccs/alz.2.ccs.bam
md5sum: b9c8093b362a07b575d52592b19fc909
- path: output/pbccs/alz.2.ccs.bam.pbi
md5sum: 78d015230a8c957a24338581efda4e55
- path: output/pbccs/alz.2.ccs_report.json
contains: ['Created by pbcopper v1.8.0']
- path: output/pbccs/alz.2.ccs_report.txt
md5sum: db379e9299295679f4ca7eeb37011f08
- path: output/pbccs/alz.2.zmw_metrics.json.gz
contains: ['zmws']
- path: output/pbccs/alz.chunk2.bam
md5sum: d1a0266d5df64b74409a21981071a1c6
- path: output/pbccs/alz.chunk2.bam.pbi
md5sum: 582a4500ddcb3f4a24a443192620d039
- path: output/pbccs/alz.metrics.json.gz
contains: [ 'zmws' ]
- path: output/pbccs/alz.report.json
contains: [ 'Created by pbcopper' ]
- path: output/pbccs/alz.report.txt
md5sum: bbc5bd7a1269345cf7a7f3d4c746024b