mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Add singularity containers for rnaseq pipeline modules
This commit is contained in:
drpatelh
parent
5561fb58d8
commit
047dbde0af
33 changed files with 208 additions and 77 deletions
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@ -11,8 +11,12 @@ process FASTQC {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
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container "quay.io/biocontainers/fastqc:0.11.9--0"
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conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
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} else {
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container "quay.io/biocontainers/fastqc:0.11.9--0"
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}
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input:
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tuple val(meta), path(reads)
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@ -10,8 +10,12 @@ process GFFREAD {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
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container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
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conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
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} else {
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container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
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}
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input:
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path gff
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@ -13,9 +13,13 @@ process HISAT2_ALIGN {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
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container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
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}
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input:
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tuple val(meta), path(reads)
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path index
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@ -12,8 +12,12 @@ process HISAT2_BUILD {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
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} else {
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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}
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input:
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path fasta
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@ -11,9 +11,13 @@ process HISAT2_EXTRACTSPLICESITES {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
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} else {
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container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
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}
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input:
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path gtf
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@ -10,9 +10,13 @@ process PICARD_MARKDUPLICATES {
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::picard=2.23.8" : null)
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container "quay.io/biocontainers/picard:2.23.8--0"
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conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
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} else {
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container "quay.io/biocontainers/picard:2.23.9--0"
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}
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input:
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tuple val(meta), path(bam)
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@ -12,9 +12,13 @@ process PRESEQ_LCEXTRAP {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
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container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
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conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
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} else {
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container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process QUALIMAP_RNASEQ {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
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container "quay.io/biocontainers/qualimap:2.2.2d--1"
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conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
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} else {
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container "quay.io/biocontainers/qualimap:2.2.2d--1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEM_CALCULATEEXPRESSION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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}
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input:
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tuple val(meta), path(reads)
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@ -11,8 +11,12 @@ process RSEM_PREPAREREFERENCE {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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}
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input:
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path fasta
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@ -11,8 +11,12 @@ process RSEQC_BAMSTAT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_INFEREXPERIMENT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_INNERDISTANCE {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_JUNCTIONANNOTATION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_JUNCTIONSATURATION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_READDISTRIBUTION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process RSEQC_READDUPLICATION {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
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} else {
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container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
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}
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input:
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tuple val(meta), path(bam)
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@ -11,8 +11,12 @@ process SALMON_INDEX {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
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container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
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conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
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} else {
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container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
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}
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input:
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path genome_fasta
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@ -38,10 +42,10 @@ process SALMON_INDEX {
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salmon \\
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index \\
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--threads $task.cpus \\
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-t gentrome.fa \\
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-t $gentrome \\
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-d decoys.txt \\
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$options.args \\
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-i salmon
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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"""
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}
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}
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@ -11,8 +11,12 @@ process SALMON_QUANT {
|
|||
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::salmon=1.3.0" : null)
|
||||
container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
|
||||
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -9,8 +9,12 @@ process SAMTOOLS_FLAGSTAT {
|
|||
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::samtools=1.10" : null)
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
||||
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:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -9,8 +9,12 @@ process SAMTOOLS_IDXSTATS {
|
|||
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::samtools=1.10" : null)
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
||||
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:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -9,8 +9,12 @@ process SAMTOOLS_INDEX {
|
|||
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::samtools=1.10" : null)
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
||||
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:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -11,8 +11,12 @@ process SAMTOOLS_SORT {
|
|||
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::samtools=1.10" : null)
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
||||
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:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -9,9 +9,13 @@ process SAMTOOLS_STATS {
|
|||
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::samtools=1.10" : null)
|
||||
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
||||
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:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
||||
|
|
|
|||
|
|
@ -11,9 +11,13 @@ process SORTMERNA {
|
|||
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::sortmerna=4.2.0" : null)
|
||||
container "quay.io/biocontainers/sortmerna:4.2.0--0"
|
||||
|
||||
conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/sortmerna:4.2.0--0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -12,8 +12,13 @@ process STAR_ALIGN {
|
|||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
}
|
||||
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -12,8 +12,12 @@ process STAR_GENOMEGENERATE {
|
|||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/star:2.6.1d--0"
|
||||
}
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -11,9 +11,12 @@ process STRINGTIE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
|
||||
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
|
||||
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -11,9 +11,12 @@ process SUBREAD_FEATURECOUNTS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
|
||||
container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
|
||||
conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams), path(annotation)
|
||||
|
|
|
|||
|
|
@ -11,8 +11,12 @@ process TRIMGALORE {
|
|||
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::trim-galore=0.6.6" : null)
|
||||
container "quay.io/biocontainers/trim-galore:0.6.6--0"
|
||||
conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/trim-galore:0.6.6--0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -13,9 +13,13 @@ process UCSC_BEDGRAPHTOBIGWIG {
|
|||
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::ucsc-bedgraphtobigwig=377" : null)
|
||||
container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_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
|
||||
|
|
|
|||
|
|
@ -11,8 +11,12 @@ process UMITOOLS_DEDUP {
|
|||
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::umi_tools=1.0.1" : null)
|
||||
container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
|
||||
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -11,8 +11,12 @@ process UMITOOLS_EXTRACT {
|
|||
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::umi_tools=1.0.1" : null)
|
||||
container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
|
||||
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
Loading…
Reference in a new issue