Split preseq lcextrap and ccurve (#1440)

* fix(preseq): Update lcextrap file name

* chore(preseq): Bump lcextrap image

* feat: Initialize preseq c_curve

* docs(preseq): Update documentation
This commit is contained in:
Edmund Miller 2022-03-25 12:11:40 -05:00 committed by GitHub
parent a066456735
commit 7111e571cc
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9 changed files with 154 additions and 12 deletions

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@ -0,0 +1,40 @@
process PRESEQ_CCURVE {
tag "$meta.id"
label 'process_medium'
label 'error_ignore'
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.c_curve.txt"), emit: c_curve
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired_end = meta.single_end ? '' : '-pe'
"""
preseq \\
c_curve \\
$args \\
$paired_end \\
-output ${prefix}.c_curve.txt \\
$bam
cp .command.err ${prefix}.command.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
}

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@ -0,0 +1,48 @@
name: preseq_ccurve
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
keywords:
- preseq
- library
- complexity
tools:
- preseq:
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
homepage: http://smithlabresearch.org/software/preseq/
documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
tool_dev_url: https://github.com/smithlabcode/preseq
doi: ""
licence: ["GPL"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
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"
- ccurve:
type: file
description: File containing output of Preseq c curve
pattern: "*.{c_curve.txt}"
- log:
type: file
description: Log file containing stderr produced by Preseq
pattern: "*.{log}"
authors:
- "@drpatelh"
- "@Emiller88"

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@ -5,16 +5,16 @@ process PRESEQ_LCEXTRAP {
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1' :
'quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1' }"
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -28,7 +28,7 @@ process PRESEQ_LCEXTRAP {
lc_extrap \\
$args \\
$paired_end \\
-output ${prefix}.ccurve.txt \\
-output ${prefix}.lc_extrap.txt \\
$bam
cp .command.err ${prefix}.command.log

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@ -8,8 +8,8 @@ tools:
- preseq:
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
homepage: http://smithlabresearch.org/software/preseq/
documentation: None
tool_dev_url: None
documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
tool_dev_url: https://github.com/smithlabcode/preseq
doi: ""
licence: ["GPL"]
@ -34,10 +34,10 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- ccurve:
- lc_extrap:
type: file
description: File containing output of Preseq lcextrap
pattern: "*.{ccurve.txt}"
pattern: "*.{lc_extrap.txt}"
- log:
type: file
description: Log file containing stderr produced by Preseq
@ -45,3 +45,4 @@ output:
authors:
- "@drpatelh"
- "@Emiller88"

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@ -1367,6 +1367,10 @@ porechop:
- modules/porechop/**
- tests/modules/porechop/**
preseq/ccurve:
- modules/preseq/ccurve/**
- tests/modules/preseq/ccurve/**
preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**

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@ -0,0 +1,25 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PRESEQ_CCURVE } from '../../../../modules/preseq/ccurve/main.nf'
workflow test_preseq_ccurve_single_end {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
PRESEQ_CCURVE ( input )
}
workflow test_preseq_ccurve_paired_end {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
PRESEQ_CCURVE ( input )
}

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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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@ -0,0 +1,19 @@
- name: preseq ccurve single-end
command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_single_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
tags:
- preseq
- preseq/ccurve
files:
- path: output/preseq/test.c_curve.txt
md5sum: cf4743abdd355595d6ec1fb3f38e66e5
- path: output/preseq/test.command.log
- name: preseq ccurve paired-end
command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
tags:
- preseq
- preseq/ccurve
files:
- path: output/preseq/test.c_curve.txt
md5sum: cf4743abdd355595d6ec1fb3f38e66e5
- path: output/preseq/test.command.log

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@ -4,7 +4,7 @@
- preseq
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
- path: output/preseq/test.lc_extrap.txt
md5sum: 1fa5cdd601079329618f61660bee00de
- path: output/preseq/test.command.log
@ -14,6 +14,6 @@
- preseq
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
- path: output/preseq/test.lc_extrap.txt
md5sum: 10e5ea860e87fb6f5dc10f4f20c62040
- path: output/preseq/test.command.log