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Commit 50ec0d49 authored by Adam Talbot's avatar Adam Talbot
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Update local modules

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with 22 additions and 22 deletions
...@@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS { ...@@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS {
conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }" 'biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
input: input:
tuple val(meta), path(cool), val(resolution) tuple val(meta), path(cool), val(resolution)
......
...@@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION { ...@@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION {
conda "bioconda::cooltools=0.5.1" conda "bioconda::cooltools=0.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' : 'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }" 'biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
input: input:
tuple val(meta), path(cool) tuple val(meta), path(cool)
......
...@@ -8,7 +8,7 @@ process HIC_FIND_TADS { ...@@ -8,7 +8,7 @@ process HIC_FIND_TADS {
conda "bioconda::hicexplorer=3.7.2" conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' : 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input: input:
tuple val(meta), path(cool) tuple val(meta), path(cool)
......
...@@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS { ...@@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS {
conda "bioconda::hicexplorer=3.7.2" conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' : 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }" 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input: input:
tuple val(meta), path(cool) tuple val(meta), path(cool)
......
...@@ -5,7 +5,7 @@ process MERGE_BOWTIE2{ ...@@ -5,7 +5,7 @@ process MERGE_BOWTIE2{
conda "bioconda::samtools=1.15.1" conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" 'biocontainers/samtools:1.15.1--h1170115_0' }"
input: input:
tuple val(meta), path(bam1), path(bam2) tuple val(meta), path(bam1), path(bam2)
......
...@@ -5,7 +5,7 @@ process BUILD_CONTACT_MAPS{ ...@@ -5,7 +5,7 @@ process BUILD_CONTACT_MAPS{
conda "conda-forge::sed=4.7" conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'quay.io/nfcore/ubuntu:20.04' }"
input: input:
tuple val(meta), path(vpairs), val(resolution) tuple val(meta), path(vpairs), val(resolution)
......
...@@ -5,7 +5,7 @@ process COMBINE_MATES { ...@@ -5,7 +5,7 @@ process COMBINE_MATES {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0" conda "conda-forge::python=3.9 bioconda::pysam=0.19.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
......
...@@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE { ...@@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE {
conda "bioconda::samtools=1.15.1" conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' : 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" 'biocontainers/samtools:1.15.1--h1170115_0' }"
input: input:
......
...@@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS { ...@@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS {
conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3" conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
......
...@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION { ...@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
......
...@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE { ...@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
......
...@@ -5,7 +5,7 @@ process HICPRO2PAIRS { ...@@ -5,7 +5,7 @@ process HICPRO2PAIRS {
conda "bioconda::pairix=0.3.7" conda "bioconda::pairix=0.3.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' : 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }" 'biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input: input:
tuple val(meta), path(vpairs) tuple val(meta), path(vpairs)
......
...@@ -5,7 +5,7 @@ process MERGE_STATS { ...@@ -5,7 +5,7 @@ process MERGE_STATS {
conda "conda-forge::python=3.9" conda "conda-forge::python=3.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), path(fstat) tuple val(meta), path(fstat)
......
...@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION { ...@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION {
conda "conda-forge::gawk=5.1.0" conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'nfcore/ubuntu:20.04' }"
input: input:
tuple val(meta), path(vpairs) tuple val(meta), path(vpairs)
......
...@@ -5,7 +5,7 @@ process ICE_NORMALIZATION{ ...@@ -5,7 +5,7 @@ process ICE_NORMALIZATION{
conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}" 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input: input:
tuple val(meta), val(res), path(rmaps), path(bed) tuple val(meta), val(res), path(rmaps), path(bed)
......
...@@ -5,7 +5,7 @@ process TRIM_READS { ...@@ -5,7 +5,7 @@ process TRIM_READS {
conda "conda-forge::sed=4.7" conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'nfcore/ubuntu:20.04' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
......
...@@ -4,7 +4,7 @@ process MULTIQC { ...@@ -4,7 +4,7 @@ process MULTIQC {
conda "bioconda::multiqc=1.13" conda "bioconda::multiqc=1.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" 'biocontainers/multiqc:1.13--pyhdfd78af_0' }"
input: input:
path multiqc_config path multiqc_config
......
...@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { ...@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
conda "conda-forge::python=3.8.3" conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }" 'biocontainers/python:3.8.3' }"
input: input:
path samplesheet path samplesheet
......
...@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP { ...@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP {
conda "conda-forge::gawk=5.1.0" conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }" 'nfcore/ubuntu:20.04' }"
input: input:
tuple val(meta), path(bedpe) tuple val(meta), path(bedpe)
......
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