From 1d30e2c21affedc742680e8e04d60c6481d9cd11 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 14 Oct 2020 18:59:25 +0100 Subject: [PATCH] Update tools not in rnaseq pipeline too --- git_update.sh | 4 +++ software/SOFTWARE/TOOL/main.nf | 34 +++++++++++-------- software/bwa/index/main.nf | 21 +++++++----- software/bwa/mem/main.nf | 25 ++++++++------ software/deeptools/computematrix/main.nf | 23 +++++++------ software/deeptools/plotfingerprint/main.nf | 23 +++++++------ software/deeptools/plotheatmap/main.nf | 23 +++++++------ software/deeptools/plotprofile/main.nf | 23 +++++++------ software/homer/annotatepeaks/main.nf | 21 +++++++----- software/macs2/callpeak/main.nf | 23 +++++++------ software/phantompeakqualtools/main.nf | 21 +++++++----- .../picard/collectmultiplemetrics/main.nf | 21 +++++++----- software/picard/markduplicates/main.nf | 23 +++++++------ software/picard/mergesamfiles/main.nf | 23 +++++++------ software/ucsc/bedgraphtobigwig/main.nf | 21 +++++++----- 15 files changed, 188 insertions(+), 141 deletions(-) create mode 100755 git_update.sh diff --git a/git_update.sh b/git_update.sh new file mode 100755 index 00000000..8515b482 --- /dev/null +++ b/git_update.sh @@ -0,0 +1,4 @@ + +git pull +git pull upstream master +git push diff --git a/software/SOFTWARE/TOOL/main.nf b/software/SOFTWARE/TOOL/main.nf index 94abc58f..e87ea87d 100644 --- a/software/SOFTWARE/TOOL/main.nf +++ b/software/SOFTWARE/TOOL/main.nf @@ -10,7 +10,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' // TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119). // TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. // All other parameters MUST be provided as a string i.e. "options.args" -// where "options" is a Groovy Map that MUST be provided in the "input:" section of the process. +// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow. // Any parameters that need to be evaluated in the context of a particular sample // e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. // TODO nf-core: Software that can be piped together SHOULD be added to separate module files @@ -18,6 +18,9 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' // e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM. // TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue. +params.options = [:] +def options = initOptions(params.options) + // TODO nf-core: Process name MUST be all uppercase, // "SOFTWARE" and (ideally) "TOOL" MUST be all one word separated by an "_". process SOFTWARE_TOOL { @@ -31,18 +34,22 @@ process SOFTWARE_TOOL { mode: params.publish_dir_mode, // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section // change "publish_id:meta.id" to initialise an empty string e.g. "publish_id:''". - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + // TODO nf-core: List required Conda packages. + // Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below. + // Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement. + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) // TODO nf-core: Fetch "docker pull" address for latest BioContainer image of software: e.g. https://biocontainers.pro/#/tools/samtools // Click on the Pacakages and Containers tab, sort by Version and get the portion of the link after the docker pull command where Type is Docker. // You may need to double-check that you are using the latest version of the software because you may find that containers for older versions have been rebuilt more recently. // If required, multi-tool containers may also be available and are usually named to start with "mulled". - container "quay.io/biocontainers/samtools:1.10--h9402c20_2" - - // TODO nf-core: List required Conda packages. - // Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below. - // Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement. - conda (params.conda ? "bioconda::samtools=1.10" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2" + } else { + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" + } input: // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" @@ -52,9 +59,7 @@ process SOFTWARE_TOOL { // TODO nf-core: Where applicable please provide/convert compressed files as input/output // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. tuple val(meta), path(reads) - // TODO nf-core: List additional required input channels/values here - val options - + output: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version) @@ -64,19 +69,18 @@ process SOFTWARE_TOOL { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section delete the line below - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 // If the software is unable to output a version number on the command-line then it can be manually specified // e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter // using the Nextflow "task" variable e.g. "--threads $task.cpus" // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) """ software tool \\ - $ioptions.args \\ + $options.args \\ --threads $task.cpus \\ $reads \\ > ${prefix}.bam diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf index 537e096a..2a647b17 100644 --- a/software/bwa/index/main.nf +++ b/software/bwa/index/main.nf @@ -1,31 +1,34 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process BWA_INDEX { tag "$fasta" label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } - container "biocontainers/bwa:v0.7.17_cv1" - //container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7" - - conda (params.conda ? "bioconda::bwa=0.7.17" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7" + } else { + container "biocontainers/bwa:v0.7.17_cv1" + } input: path fasta - val options - + output: path "${fasta}.*" , emit: index path "*.version.txt", emit: version script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) """ - bwa index $ioptions.args $fasta + bwa index $options.args $fasta echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt """ } diff --git a/software/bwa/mem/main.nf b/software/bwa/mem/main.nf index 73eadaf8..78e0f968 100644 --- a/software/bwa/mem/main.nf +++ b/software/bwa/mem/main.nf @@ -1,41 +1,44 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process BWA_MEM { tag "$meta.id" label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" - //container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" - - conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" + } else { + container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" + } input: tuple val(meta), path(reads) path index path fasta - val options - + output: tuple val(meta), path("*.bam"), emit: bam path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ bwa mem \\ - $ioptions.args \\ + $options.args \\ $read_group \\ -t $task.cpus \\ $fasta \\ $reads \\ - | samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam - + | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam - echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt """ diff --git a/software/deeptools/computematrix/main.nf b/software/deeptools/computematrix/main.nf index 27e3b042..4eb6453f 100644 --- a/software/deeptools/computematrix/main.nf +++ b/software/deeptools/computematrix/main.nf @@ -1,23 +1,27 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process DEEPTOOLS_COMPUTEMATRIX { tag "$meta.id" label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/deeptools:3.4.3--py_0" - //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" - - conda (params.conda ? "bioconda::deeptools=3.4.3" : null) + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.4.3--py_0" + } input: tuple val(meta), path(bigwig) path bed - val options - + output: tuple val(meta), path("*.mat.gz") , emit: matrix tuple val(meta), path("*.mat.tab"), emit: table @@ -25,11 +29,10 @@ process DEEPTOOLS_COMPUTEMATRIX { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ computeMatrix \\ - $ioptions.args \\ + $options.args \\ --regionsFileName $bed \\ --scoreFileName $bigwig \\ --outFileName ${prefix}.computeMatrix.mat.gz \\ diff --git a/software/deeptools/plotfingerprint/main.nf b/software/deeptools/plotfingerprint/main.nf index 57b56a06..2815a13c 100644 --- a/software/deeptools/plotfingerprint/main.nf +++ b/software/deeptools/plotfingerprint/main.nf @@ -1,22 +1,26 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process DEEPTOOLS_PLOTFINGERPRINT { tag "$meta.id" label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/deeptools:3.4.3--py_0" - //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" - - conda (params.conda ? "bioconda::deeptools=3.4.3" : null) + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.4.3--py_0" + } input: tuple val(meta), path(bams), path(bais) - val options - + output: tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.raw.txt") , emit: matrix @@ -25,12 +29,11 @@ process DEEPTOOLS_PLOTFINGERPRINT { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : '' """ plotFingerprint \\ - $ioptions.args \\ + $options.args \\ $extend \\ --bamfiles ${bams.join(' ')} \\ --plotFile ${prefix}.plotFingerprint.pdf \\ diff --git a/software/deeptools/plotheatmap/main.nf b/software/deeptools/plotheatmap/main.nf index ca8bf08f..7d3d01bc 100644 --- a/software/deeptools/plotheatmap/main.nf +++ b/software/deeptools/plotheatmap/main.nf @@ -1,22 +1,26 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process DEEPTOOLS_PLOTHEATMAP { tag "$meta.id" label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/deeptools:3.4.3--py_0" - //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" - - conda (params.conda ? "bioconda::deeptools=3.4.3" : null) + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.4.3--py_0" + } input: tuple val(meta), path(matrix) - val options - + output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table @@ -24,11 +28,10 @@ process DEEPTOOLS_PLOTHEATMAP { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ plotHeatmap \\ - $ioptions.args \\ + $options.args \\ --matrixFile $matrix \\ --outFileName ${prefix}.plotHeatmap.pdf \\ --outFileNameMatrix ${prefix}.plotHeatmap.mat.tab diff --git a/software/deeptools/plotprofile/main.nf b/software/deeptools/plotprofile/main.nf index 6a976f7f..4c6865ea 100644 --- a/software/deeptools/plotprofile/main.nf +++ b/software/deeptools/plotprofile/main.nf @@ -1,22 +1,26 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process DEEPTOOLS_PLOTPROFILE { tag "$meta.id" label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/deeptools:3.4.3--py_0" - //container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" - - conda (params.conda ? "bioconda::deeptools=3.4.3" : null) + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.4.3--py_0" + } input: tuple val(meta), path(matrix) - val options - + output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.tab"), emit: table @@ -24,11 +28,10 @@ process DEEPTOOLS_PLOTPROFILE { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ plotProfile \\ - $ioptions.args \\ + $options.args \\ --matrixFile $matrix \\ --outFileName ${prefix}.plotProfile.pdf \\ --outFileNameData ${prefix}.plotProfile.tab diff --git a/software/homer/annotatepeaks/main.nf b/software/homer/annotatepeaks/main.nf index 98d234b0..9bdf0494 100644 --- a/software/homer/annotatepeaks/main.nf +++ b/software/homer/annotatepeaks/main.nf @@ -1,6 +1,9 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + def VERSION = '4.11' process HOMER_ANNOTATEPEAKS { @@ -8,18 +11,19 @@ process HOMER_ANNOTATEPEAKS { label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2" - //container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2" - - conda (params.conda ? "bioconda::homer=4.11" : null) + conda (params.enable_conda ? "bioconda::homer=4.11" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2" + } else { + container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2" + } input: tuple val(meta), path(peak) path fasta path gtf - val options output: tuple val(meta), path("*annotatePeaks.txt"), emit: txt @@ -27,13 +31,12 @@ process HOMER_ANNOTATEPEAKS { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ annotatePeaks.pl \\ $peak \\ $fasta \\ - $ioptions.args \\ + $options.args \\ -gtf $gtf \\ -cpu $task.cpus \\ > ${prefix}.annotatePeaks.txt diff --git a/software/macs2/callpeak/main.nf b/software/macs2/callpeak/main.nf index e9a2a9c1..b932d6cb 100644 --- a/software/macs2/callpeak/main.nf +++ b/software/macs2/callpeak/main.nf @@ -1,23 +1,27 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process MACS2_CALLPEAK { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0" - //container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0" - - conda (params.conda ? "bioconda::macs2=2.2.7.1" : null) + conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py37h516909a_0" + } else { + container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0" + } input: tuple val(meta), path(ipbam), path(controlbam) val macs2_gsize - val options - + output: tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak tuple val(meta), path("*.xls") , emit: xls @@ -29,14 +33,13 @@ process MACS2_CALLPEAK { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def format = meta.single_end ? 'BAM' : 'BAMPE' def control = controlbam ? "--control $controlbam" : '' """ macs2 \\ callpeak \\ - $ioptions.args \\ + $options.args \\ --gsize $macs2_gsize \\ --format $format \\ --name $prefix \\ diff --git a/software/phantompeakqualtools/main.nf b/software/phantompeakqualtools/main.nf index f9471dc6..a3d32a3e 100644 --- a/software/phantompeakqualtools/main.nf +++ b/software/phantompeakqualtools/main.nf @@ -1,6 +1,9 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + def VERSION = '1.2.2' process PHANTOMPEAKQUALTOOLS { @@ -8,17 +11,18 @@ process PHANTOMPEAKQUALTOOLS { label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0" - //container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0" - - conda (params.conda ? "bioconda::phantompeakqualtools=1.2.2" : null) + conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0" + } else { + container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0" + } input: tuple val(meta), path(bam) - val options - + output: tuple val(meta), path("*.out") , emit: spp tuple val(meta), path("*.pdf") , emit: pdf @@ -27,8 +31,7 @@ process PHANTOMPEAKQUALTOOLS { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ RUN_SPP=`which run_spp.R` Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus diff --git a/software/picard/collectmultiplemetrics/main.nf b/software/picard/collectmultiplemetrics/main.nf index 248da6c5..ff0c0835 100644 --- a/software/picard/collectmultiplemetrics/main.nf +++ b/software/picard/collectmultiplemetrics/main.nf @@ -1,22 +1,26 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process PICARD_COLLECTMULTIPLEMETRICS { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/picard:2.23.6--0" - //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" - - conda (params.conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + } else { + container "quay.io/biocontainers/picard:2.23.6--0" + } input: tuple val(meta), path(bam) path fasta - val options output: tuple val(meta), path("*_metrics"), emit: metrics @@ -25,8 +29,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -37,7 +40,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { picard \\ -Xmx${avail_mem}g \\ CollectMultipleMetrics \\ - $ioptions.args \\ + $options.args \\ INPUT=$bam \\ OUTPUT=${prefix}.CollectMultipleMetrics \\ REFERENCE_SEQUENCE=$fasta diff --git a/software/picard/markduplicates/main.nf b/software/picard/markduplicates/main.nf index 2e484115..924f8a94 100644 --- a/software/picard/markduplicates/main.nf +++ b/software/picard/markduplicates/main.nf @@ -1,22 +1,26 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/picard:2.23.6--0" - //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" - - conda (params.conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + } else { + container "quay.io/biocontainers/picard:2.23.6--0" + } input: tuple val(meta), path(bam) - val options - + output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.metrics.txt"), emit: metrics @@ -24,8 +28,7 @@ process PICARD_MARKDUPLICATES { script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -36,7 +39,7 @@ process PICARD_MARKDUPLICATES { picard \\ -Xmx${avail_mem}g \\ MarkDuplicates \\ - $ioptions.args \\ + $options.args \\ INPUT=$bam \\ OUTPUT=${prefix}.bam \\ METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt diff --git a/software/picard/mergesamfiles/main.nf b/software/picard/mergesamfiles/main.nf index 403933a3..295cc259 100644 --- a/software/picard/mergesamfiles/main.nf +++ b/software/picard/mergesamfiles/main.nf @@ -1,30 +1,33 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + process PICARD_MERGESAMFILES { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/picard:2.23.6--0" - //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" - - conda (params.conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + } else { + container "quay.io/biocontainers/picard:2.23.6--0" + } input: tuple val(meta), path(bams) - val options - + output: tuple val(meta), path("*.bam"), emit: bam path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def bam_files = bams.sort() def avail_mem = 3 if (!task.memory) { @@ -37,7 +40,7 @@ process PICARD_MERGESAMFILES { picard \\ -Xmx${avail_mem}g \\ MergeSamFiles \\ - $ioptions.args \\ + $options.args \\ ${'INPUT='+bam_files.join(' INPUT=')} \\ OUTPUT=${prefix}.bam echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf index b21b5fe0..1d7a425f 100644 --- a/software/ucsc/bedgraphtobigwig/main.nf +++ b/software/ucsc/bedgraphtobigwig/main.nf @@ -1,6 +1,9 @@ // Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + def VERSION = '377' process UCSC_BEDRAPHTOBIGWIG { @@ -8,26 +11,26 @@ process UCSC_BEDRAPHTOBIGWIG { label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1" - //container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1" - - conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) + conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) + if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1" + } else { + container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1" + } input: tuple val(meta), path(bedgraph) path sizes - val options - + output: tuple val(meta), path("*.bigWig"), emit: bigwig path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) - def ioptions = initOptions(options) - def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig echo $VERSION > ${software}.version.txt