From a3f46865ff289455dc8483b39788279728943a53 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 12 Nov 2020 14:55:16 +0000 Subject: [PATCH] Remove Singularity image path --- software/SOFTWARE/TOOL/main.nf | 10 +++------- software/bwa/index/main.nf | 10 +++------- software/bwa/mem/main.nf | 10 +++------- 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/fastqc/main.nf | 8 ++------ software/gffread/main.nf | 8 ++------ software/hisat2/align/main.nf | 8 ++------ software/hisat2/build/main.nf | 8 ++------ software/hisat2/extractsplicesites/main.nf | 8 ++------ software/homer/annotatepeaks/main.nf | 8 ++------ software/macs2/callpeak/main.nf | 8 ++------ software/phantompeakqualtools/main.nf | 8 ++------ software/picard/collectmultiplemetrics/main.nf | 8 ++------ software/picard/markduplicates/main.nf | 8 ++------ software/picard/mergesamfiles/main.nf | 8 ++------ software/preseq/lcextrap/main.nf | 8 ++------ software/qualimap/rnaseq/main.nf | 8 ++------ software/rsem/calculateexpression/main.nf | 8 ++------ software/rsem/preparereference/main.nf | 8 ++------ software/rseqc/bamstat/main.nf | 8 ++------ software/rseqc/inferexperiment/main.nf | 8 ++------ software/rseqc/innerdistance/main.nf | 8 ++------ software/rseqc/junctionannotation/main.nf | 8 ++------ software/rseqc/junctionsaturation/main.nf | 8 ++------ software/rseqc/readdistribution/main.nf | 8 ++------ software/rseqc/readduplication/main.nf | 8 ++------ software/salmon/index/main.nf | 8 ++------ software/salmon/quant/main.nf | 8 ++------ software/samtools/flagstat/main.nf | 8 ++------ software/samtools/idxstats/main.nf | 8 ++------ software/samtools/index/main.nf | 8 ++------ software/samtools/sort/main.nf | 8 ++------ software/samtools/stats/main.nf | 8 ++------ software/sortmerna/main.nf | 8 ++------ software/star/align/main.nf | 8 ++------ software/star/genomegenerate/main.nf | 8 ++------ software/stringtie/main.nf | 8 ++------ software/subread/featurecounts/main.nf | 8 ++------ software/trimgalore/main.nf | 8 ++------ software/ucsc/bedgraphtobigwig/main.nf | 8 ++------ software/umitools/dedup/main.nf | 8 ++------ software/umitools/extract/main.nf | 8 ++------ 45 files changed, 94 insertions(+), 274 deletions(-) diff --git a/software/SOFTWARE/TOOL/main.nf b/software/SOFTWARE/TOOL/main.nf index e87ea87d..dc102024 100644 --- a/software/SOFTWARE/TOOL/main.nf +++ b/software/SOFTWARE/TOOL/main.nf @@ -39,18 +39,14 @@ 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". - 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" - } - + 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" // MUST be provided as an input via a Groovy Map called "meta". diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf index 2a647b17..6f4cbc61 100644 --- a/software/bwa/index/main.nf +++ b/software/bwa/index/main.nf @@ -11,13 +11,9 @@ 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) - 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" - } - + conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) + 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 78e0f968..ebb85f26 100644 --- a/software/bwa/mem/main.nf +++ b/software/bwa/mem/main.nf @@ -11,13 +11,9 @@ 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) - 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" - } - + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0" + input: tuple val(meta), path(reads) path index diff --git a/software/deeptools/computematrix/main.nf b/software/deeptools/computematrix/main.nf index 4eb6453f..43da2f05 100644 --- a/software/deeptools/computematrix/main.nf +++ b/software/deeptools/computematrix/main.nf @@ -11,12 +11,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + container "quay.io/biocontainers/deeptools:3.4.3--py_0" input: tuple val(meta), path(bigwig) diff --git a/software/deeptools/plotfingerprint/main.nf b/software/deeptools/plotfingerprint/main.nf index 2815a13c..b021d8eb 100644 --- a/software/deeptools/plotfingerprint/main.nf +++ b/software/deeptools/plotfingerprint/main.nf @@ -11,12 +11,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + container "quay.io/biocontainers/deeptools:3.4.3--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 7d3d01bc..2fb1d03f 100644 --- a/software/deeptools/plotheatmap/main.nf +++ b/software/deeptools/plotheatmap/main.nf @@ -11,12 +11,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + container "quay.io/biocontainers/deeptools:3.4.3--py_0" input: tuple val(meta), path(matrix) diff --git a/software/deeptools/plotprofile/main.nf b/software/deeptools/plotprofile/main.nf index 4c6865ea..e481c392 100644 --- a/software/deeptools/plotprofile/main.nf +++ b/software/deeptools/plotprofile/main.nf @@ -11,13 +11,9 @@ 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) - 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" - } - + conda (params.enable_conda ? "bioconda::deeptools=3.4.3" : null) + container "quay.io/biocontainers/deeptools:3.4.3--py_0" + input: tuple val(meta), path(matrix) diff --git a/software/fastqc/main.nf b/software/fastqc/main.nf index 64ea7b19..3edc97a1 100644 --- a/software/fastqc/main.nf +++ b/software/fastqc/main.nf @@ -11,12 +11,8 @@ process FASTQC { 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::fastqc=0.11.9" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0" - } else { - container "quay.io/biocontainers/fastqc:0.11.9--0" - } + conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + container "quay.io/biocontainers/fastqc:0.11.9--0" input: tuple val(meta), path(reads) diff --git a/software/gffread/main.nf b/software/gffread/main.nf index c364ba5d..9906f620 100644 --- a/software/gffread/main.nf +++ b/software/gffread/main.nf @@ -10,12 +10,8 @@ process GFFREAD { 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::gffread=0.12.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0" - } else { - container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0" - } + conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) + container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0" input: path gff diff --git a/software/hisat2/align/main.nf b/software/hisat2/align/main.nf index 374fcef1..d2c6fbcd 100644 --- a/software/hisat2/align/main.nf +++ b/software/hisat2/align/main.nf @@ -13,12 +13,8 @@ process HISAT2_ALIGN { 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::hisat2=2.2.0 bioconda::samtools=1.10" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0" - } else { - container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0" - } + conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0" input: tuple val(meta), path(reads) diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf index 4654d5f8..25596c89 100644 --- a/software/hisat2/build/main.nf +++ b/software/hisat2/build/main.nf @@ -12,12 +12,8 @@ process HISAT2_BUILD { 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::hisat2=2.2.0" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4" - } else { - container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4" - } + conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) + container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4" input: path fasta diff --git a/software/hisat2/extractsplicesites/main.nf b/software/hisat2/extractsplicesites/main.nf index f3278b41..bfd2cf38 100644 --- a/software/hisat2/extractsplicesites/main.nf +++ b/software/hisat2/extractsplicesites/main.nf @@ -11,12 +11,8 @@ process HISAT2_EXTRACTSPLICESITES { 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::hisat2=2.2.0" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4" - } else { - container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4" - } + conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) + container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4" input: path gtf diff --git a/software/homer/annotatepeaks/main.nf b/software/homer/annotatepeaks/main.nf index 9bdf0494..2e3696ba 100644 --- a/software/homer/annotatepeaks/main.nf +++ b/software/homer/annotatepeaks/main.nf @@ -13,12 +13,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::homer=4.11" : null) + container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2" input: tuple val(meta), path(peak) diff --git a/software/macs2/callpeak/main.nf b/software/macs2/callpeak/main.nf index b932d6cb..1096ec3b 100644 --- a/software/macs2/callpeak/main.nf +++ b/software/macs2/callpeak/main.nf @@ -11,12 +11,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) + container "quay.io/biocontainers/macs2:2.2.7.1--py37h516909a_0" input: tuple val(meta), path(ipbam), path(controlbam) diff --git a/software/phantompeakqualtools/main.nf b/software/phantompeakqualtools/main.nf index a3d32a3e..6347c527 100644 --- a/software/phantompeakqualtools/main.nf +++ b/software/phantompeakqualtools/main.nf @@ -13,12 +13,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) + 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 b9f8e496..a59b2d22 100644 --- a/software/picard/collectmultiplemetrics/main.nf +++ b/software/picard/collectmultiplemetrics/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" - } else { - container "quay.io/biocontainers/picard:2.23.8--0" - } + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) + container "quay.io/biocontainers/picard:2.23.8--0" input: tuple val(meta), path(bam) diff --git a/software/picard/markduplicates/main.nf b/software/picard/markduplicates/main.nf index 94c46b82..032a4070 100644 --- a/software/picard/markduplicates/main.nf +++ b/software/picard/markduplicates/main.nf @@ -11,12 +11,8 @@ process PICARD_MARKDUPLICATES { 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" - } else { - container "quay.io/biocontainers/picard:2.23.8--0" - } + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) + container "quay.io/biocontainers/picard:2.23.8--0" input: tuple val(meta), path(bam) diff --git a/software/picard/mergesamfiles/main.nf b/software/picard/mergesamfiles/main.nf index 09c36ebf..961595f9 100644 --- a/software/picard/mergesamfiles/main.nf +++ b/software/picard/mergesamfiles/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" - } else { - container "quay.io/biocontainers/picard:2.23.8--0" - } + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) + container "quay.io/biocontainers/picard:2.23.8--0" input: tuple val(meta), path(bams) diff --git a/software/preseq/lcextrap/main.nf b/software/preseq/lcextrap/main.nf index bb7de662..89afeda7 100644 --- a/software/preseq/lcextrap/main.nf +++ b/software/preseq/lcextrap/main.nf @@ -12,12 +12,8 @@ process PRESEQ_LCEXTRAP { 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::preseq=2.0.3" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3" - } else { - container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3" - } + conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null) + container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3" input: tuple val(meta), path(bam) diff --git a/software/qualimap/rnaseq/main.nf b/software/qualimap/rnaseq/main.nf index 7575140f..f24001e8 100644 --- a/software/qualimap/rnaseq/main.nf +++ b/software/qualimap/rnaseq/main.nf @@ -11,12 +11,8 @@ process QUALIMAP_RNASEQ { 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::qualimap=2.2.2d" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1" - } else { - container "quay.io/biocontainers/qualimap:2.2.2d--1" - } + conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) + container "quay.io/biocontainers/qualimap:2.2.2d--1" input: tuple val(meta), path(bam) diff --git a/software/rsem/calculateexpression/main.nf b/software/rsem/calculateexpression/main.nf index b5fdb336..f00d7686 100644 --- a/software/rsem/calculateexpression/main.nf +++ b/software/rsem/calculateexpression/main.nf @@ -11,12 +11,8 @@ process RSEM_CALCULATEEXPRESSION { 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::rsem=1.3.3 bioconda::star=2.7.6a" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" - } else { - container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" - } + conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) + container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" input: tuple val(meta), path(reads) diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf index 5a41728c..570eac76 100644 --- a/software/rsem/preparereference/main.nf +++ b/software/rsem/preparereference/main.nf @@ -11,12 +11,8 @@ process RSEM_PREPAREREFERENCE { 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::rsem=1.3.3 bioconda::star=2.7.6a" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" - } else { - container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" - } + conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) + container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0" input: path fasta diff --git a/software/rseqc/bamstat/main.nf b/software/rseqc/bamstat/main.nf index dfc1614d..e9a34add 100644 --- a/software/rseqc/bamstat/main.nf +++ b/software/rseqc/bamstat/main.nf @@ -11,12 +11,8 @@ process RSEQC_BAMSTAT { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/inferexperiment/main.nf b/software/rseqc/inferexperiment/main.nf index 65583fcf..79dfd4f9 100644 --- a/software/rseqc/inferexperiment/main.nf +++ b/software/rseqc/inferexperiment/main.nf @@ -11,12 +11,8 @@ process RSEQC_INFEREXPERIMENT { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/innerdistance/main.nf b/software/rseqc/innerdistance/main.nf index 4d064d57..9ace426d 100644 --- a/software/rseqc/innerdistance/main.nf +++ b/software/rseqc/innerdistance/main.nf @@ -11,12 +11,8 @@ process RSEQC_INNERDISTANCE { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/junctionannotation/main.nf b/software/rseqc/junctionannotation/main.nf index ed1ae8c6..9cc6d00f 100644 --- a/software/rseqc/junctionannotation/main.nf +++ b/software/rseqc/junctionannotation/main.nf @@ -11,12 +11,8 @@ process RSEQC_JUNCTIONANNOTATION { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/junctionsaturation/main.nf b/software/rseqc/junctionsaturation/main.nf index aa797633..a472aba5 100644 --- a/software/rseqc/junctionsaturation/main.nf +++ b/software/rseqc/junctionsaturation/main.nf @@ -11,12 +11,8 @@ process RSEQC_JUNCTIONSATURATION { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/readdistribution/main.nf b/software/rseqc/readdistribution/main.nf index f04cabbb..de99185f 100644 --- a/software/rseqc/readdistribution/main.nf +++ b/software/rseqc/readdistribution/main.nf @@ -11,12 +11,8 @@ process RSEQC_READDISTRIBUTION { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/rseqc/readduplication/main.nf b/software/rseqc/readduplication/main.nf index 4a9d17aa..4a3998da 100644 --- a/software/rseqc/readduplication/main.nf +++ b/software/rseqc/readduplication/main.nf @@ -11,12 +11,8 @@ process RSEQC_READDUPLICATION { 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::rseqc=3.0.1" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null) + container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" input: tuple val(meta), path(bam) diff --git a/software/salmon/index/main.nf b/software/salmon/index/main.nf index b9a4c51b..754818fe 100644 --- a/software/salmon/index/main.nf +++ b/software/salmon/index/main.nf @@ -11,12 +11,8 @@ process SALMON_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::salmon=1.3.0" : null) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0" - } else { - container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0" - } + conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null) + container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0" input: path fasta diff --git a/software/salmon/quant/main.nf b/software/salmon/quant/main.nf index eb2a373a..4d0ca869 100644 --- a/software/salmon/quant/main.nf +++ b/software/salmon/quant/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0" - } else { - container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0" - } + conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null) + container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0" input: tuple val(meta), path(reads) diff --git a/software/samtools/flagstat/main.nf b/software/samtools/flagstat/main.nf index 00992c60..46e95df0 100644 --- a/software/samtools/flagstat/main.nf +++ b/software/samtools/flagstat/main.nf @@ -9,12 +9,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" input: tuple val(meta), path(bam), path(bai) diff --git a/software/samtools/idxstats/main.nf b/software/samtools/idxstats/main.nf index 75ae493f..29e680df 100644 --- a/software/samtools/idxstats/main.nf +++ b/software/samtools/idxstats/main.nf @@ -9,12 +9,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" input: tuple val(meta), path(bam), path(bai) diff --git a/software/samtools/index/main.nf b/software/samtools/index/main.nf index 09a24f25..23c9ec41 100644 --- a/software/samtools/index/main.nf +++ b/software/samtools/index/main.nf @@ -9,12 +9,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" input: tuple val(meta), path(bam) diff --git a/software/samtools/sort/main.nf b/software/samtools/sort/main.nf index 17f0df57..a872e11f 100644 --- a/software/samtools/sort/main.nf +++ b/software/samtools/sort/main.nf @@ -11,12 +11,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" input: tuple val(meta), path(bam) diff --git a/software/samtools/stats/main.nf b/software/samtools/stats/main.nf index c368b4f6..e1949ee7 100644 --- a/software/samtools/stats/main.nf +++ b/software/samtools/stats/main.nf @@ -9,12 +9,8 @@ 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) - 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" - } + conda (params.enable_conda ? "bioconda::samtools=1.10" : null) + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" input: tuple val(meta), path(bam), path(bai) diff --git a/software/sortmerna/main.nf b/software/sortmerna/main.nf index c0839761..a1ea4864 100644 --- a/software/sortmerna/main.nf +++ b/software/sortmerna/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0" - } else { - container "quay.io/biocontainers/sortmerna:4.2.0--0" - } + conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null) + container "quay.io/biocontainers/sortmerna:4.2.0--0" input: tuple val(meta), path(reads) diff --git a/software/star/align/main.nf b/software/star/align/main.nf index 9b58e53c..c143ba1d 100644 --- a/software/star/align/main.nf +++ b/software/star/align/main.nf @@ -12,12 +12,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0" - } else { - container "quay.io/biocontainers/star:2.6.1d--0" - } + conda (params.enable_conda ? "bioconda::star=2.6.1d" : null) + container "quay.io/biocontainers/star:2.6.1d--0" input: tuple val(meta), path(reads) diff --git a/software/star/genomegenerate/main.nf b/software/star/genomegenerate/main.nf index 6f976273..915b5675 100644 --- a/software/star/genomegenerate/main.nf +++ b/software/star/genomegenerate/main.nf @@ -12,12 +12,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0" - } else { - container "quay.io/biocontainers/star:2.6.1d--0" - } + conda (params.enable_conda ? "bioconda::star=2.6.1d" : null) + container "quay.io/biocontainers/star:2.6.1d--0" input: path fasta diff --git a/software/stringtie/main.nf b/software/stringtie/main.nf index fc3cbd49..ba2c42bd 100644 --- a/software/stringtie/main.nf +++ b/software/stringtie/main.nf @@ -12,12 +12,8 @@ process STRINGTIE { 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) - if (workflow.containerEngine == 'singularity' && !params.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" - } + conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null) + container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0" input: tuple val(meta), path(bam) diff --git a/software/subread/featurecounts/main.nf b/software/subread/featurecounts/main.nf index 936c2ccf..e8644af5 100644 --- a/software/subread/featurecounts/main.nf +++ b/software/subread/featurecounts/main.nf @@ -12,12 +12,8 @@ process SUBREAD_FEATURECOUNTS { 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) - if (workflow.containerEngine == 'singularity' && !params.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" - } + conda (params.enable_conda ? "bioconda::subread=2.0.1" : null) + container "quay.io/biocontainers/subread:2.0.1--hed695b0_0" input: tuple val(meta), path(bams), path(annotation) diff --git a/software/trimgalore/main.nf b/software/trimgalore/main.nf index 0a32825e..742ffaf5 100644 --- a/software/trimgalore/main.nf +++ b/software/trimgalore/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.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" - } + conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null) + container "quay.io/biocontainers/trim-galore:0.6.6--0" input: tuple val(meta), path(reads) diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf index 1d7a425f..f8eef0d9 100644 --- a/software/ucsc/bedgraphtobigwig/main.nf +++ b/software/ucsc/bedgraphtobigwig/main.nf @@ -13,12 +13,8 @@ process UCSC_BEDRAPHTOBIGWIG { 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) - 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" - } + conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) + container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1" input: tuple val(meta), path(bedgraph) diff --git a/software/umitools/dedup/main.nf b/software/umitools/dedup/main.nf index abeab49a..8348cda4 100644 --- a/software/umitools/dedup/main.nf +++ b/software/umitools/dedup/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null) + container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1" input: tuple val(meta), path(bam), path(bai) diff --git a/software/umitools/extract/main.nf b/software/umitools/extract/main.nf index 34cb3e3c..d04f2e3d 100644 --- a/software/umitools/extract/main.nf +++ b/software/umitools/extract/main.nf @@ -11,12 +11,8 @@ 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) - if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1" - } else { - container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1" - } + conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null) + container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1" input: tuple val(meta), path(reads)