From 99a2364a267f726cccf218379045c1725799b6e7 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 14 Dec 2020 00:05:48 +0000 Subject: [PATCH] Update all other modules --- software/SOFTWARE/TOOL/main.nf | 8 ++++++-- software/bwa/index/main.nf | 10 +++++++--- software/bwa/mem/main.nf | 8 ++++++-- software/deeptools/computematrix/main.nf | 8 ++++++-- software/deeptools/plotfingerprint/main.nf | 8 ++++++-- software/deeptools/plotheatmap/main.nf | 8 ++++++-- software/deeptools/plotprofile/main.nf | 10 +++++++--- software/homer/annotatepeaks/main.nf | 8 ++++++-- software/macs2/callpeak/main.nf | 8 ++++++-- software/multiqc/main.nf | 8 ++++++-- software/phantompeakqualtools/main.nf | 10 +++++++--- software/picard/collectmultiplemetrics/main.nf | 8 ++++++-- software/picard/mergesamfiles/main.nf | 8 ++++++-- 13 files changed, 81 insertions(+), 29 deletions(-) diff --git a/software/SOFTWARE/TOOL/main.nf b/software/SOFTWARE/TOOL/main.nf index dc102024..4c00cc27 100644 --- a/software/SOFTWARE/TOOL/main.nf +++ b/software/SOFTWARE/TOOL/main.nf @@ -39,13 +39,17 @@ process SOFTWARE_TOOL { // 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) + 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" + if (workflow.containerEngine == 'singularity' && !params.singularity_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" diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf index 6f4cbc61..7b1e6ff9 100644 --- a/software/bwa/index/main.nf +++ b/software/bwa/index/main.nf @@ -11,9 +11,13 @@ process BWA_INDEX { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } - conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) - container "biocontainers/bwa:v0.7.17_cv1" - + conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_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 diff --git a/software/bwa/mem/main.nf b/software/bwa/mem/main.nf index ebb85f26..2bf3b932 100644 --- a/software/bwa/mem/main.nf +++ b/software/bwa/mem/main.nf @@ -11,8 +11,12 @@ process BWA_MEM { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) - container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_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) diff --git a/software/deeptools/computematrix/main.nf b/software/deeptools/computematrix/main.nf index 43da2f05..9c51282f 100644 --- a/software/deeptools/computematrix/main.nf +++ b/software/deeptools/computematrix/main.nf @@ -11,8 +11,12 @@ process DEEPTOOLS_COMPUTEMATRIX { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) - container "quay.io/biocontainers/deeptools:3.4.3--py_0" + conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.5.0--py_0" + } input: tuple val(meta), path(bigwig) diff --git a/software/deeptools/plotfingerprint/main.nf b/software/deeptools/plotfingerprint/main.nf index b021d8eb..72a0e596 100644 --- a/software/deeptools/plotfingerprint/main.nf +++ b/software/deeptools/plotfingerprint/main.nf @@ -11,8 +11,12 @@ process DEEPTOOLS_PLOTFINGERPRINT { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) - container "quay.io/biocontainers/deeptools:3.4.3--py_0" + conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.5.0--py_0" + } input: tuple val(meta), path(bams), path(bais) diff --git a/software/deeptools/plotheatmap/main.nf b/software/deeptools/plotheatmap/main.nf index 2fb1d03f..d245922f 100644 --- a/software/deeptools/plotheatmap/main.nf +++ b/software/deeptools/plotheatmap/main.nf @@ -11,8 +11,12 @@ process DEEPTOOLS_PLOTHEATMAP { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) - container "quay.io/biocontainers/deeptools:3.4.3--py_0" + conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.5.0--py_0" + } input: tuple val(meta), path(matrix) diff --git a/software/deeptools/plotprofile/main.nf b/software/deeptools/plotprofile/main.nf index e481c392..0657408b 100644 --- a/software/deeptools/plotprofile/main.nf +++ b/software/deeptools/plotprofile/main.nf @@ -11,9 +11,13 @@ process DEEPTOOLS_PLOTPROFILE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) - container "quay.io/biocontainers/deeptools:3.4.3--py_0" - + conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0" + } else { + container "quay.io/biocontainers/deeptools:3.5.0--py_0" + } + input: tuple val(meta), path(matrix) diff --git a/software/homer/annotatepeaks/main.nf b/software/homer/annotatepeaks/main.nf index 2e3696ba..1e03eb64 100644 --- a/software/homer/annotatepeaks/main.nf +++ b/software/homer/annotatepeaks/main.nf @@ -13,8 +13,12 @@ process HOMER_ANNOTATEPEAKS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::homer=4.11" : null) - container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2" + conda (params.enable_conda ? "bioconda::homer=4.11" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3" + } else { + container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3" + } input: tuple val(meta), path(peak) diff --git a/software/macs2/callpeak/main.nf b/software/macs2/callpeak/main.nf index 1096ec3b..0206fe85 100644 --- a/software/macs2/callpeak/main.nf +++ b/software/macs2/callpeak/main.nf @@ -11,8 +11,12 @@ process MACS2_CALLPEAK { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) - container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0" + conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1" + } else { + container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1" + } input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/software/multiqc/main.nf b/software/multiqc/main.nf index 09d223fc..ff1175fc 100644 --- a/software/multiqc/main.nf +++ b/software/multiqc/main.nf @@ -10,8 +10,12 @@ process MULTIQC { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') } - conda (params.enable_conda ? "bioconda::multiqc=1.9" : null) - container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0" + conda (params.enable_conda ? "bioconda::multiqc=1.9" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0" + } else { + container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0" + } input: path multiqc_files diff --git a/software/phantompeakqualtools/main.nf b/software/phantompeakqualtools/main.nf index 6347c527..1e9e1740 100644 --- a/software/phantompeakqualtools/main.nf +++ b/software/phantompeakqualtools/main.nf @@ -13,9 +13,13 @@ process PHANTOMPEAKQUALTOOLS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) - container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0" - + conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_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) diff --git a/software/picard/collectmultiplemetrics/main.nf b/software/picard/collectmultiplemetrics/main.nf index a59b2d22..a4eb4e5f 100644 --- a/software/picard/collectmultiplemetrics/main.nf +++ b/software/picard/collectmultiplemetrics/main.nf @@ -11,8 +11,12 @@ process PICARD_COLLECTMULTIPLEMETRICS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) - container "quay.io/biocontainers/picard:2.23.8--0" + conda (params.enable_conda ? "bioconda::picard=2.23.9" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0" + } else { + container "quay.io/biocontainers/picard:2.23.9--0" + } input: tuple val(meta), path(bam) diff --git a/software/picard/mergesamfiles/main.nf b/software/picard/mergesamfiles/main.nf index 961595f9..2c356dff 100644 --- a/software/picard/mergesamfiles/main.nf +++ b/software/picard/mergesamfiles/main.nf @@ -11,8 +11,12 @@ process PICARD_MERGESAMFILES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) - container "quay.io/biocontainers/picard:2.23.8--0" + conda (params.enable_conda ? "bioconda::picard=2.23.9" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0" + } else { + container "quay.io/biocontainers/picard:2.23.9--0" + } input: tuple val(meta), path(bams)