From 50ec0d49fd73682c3d7850fe2cafe64fbec0249c Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 22 May 2023 17:47:31 +0100
Subject: [PATCH] Update local modules
---
modules/local/cooltools/eigscis.nf | 2 +-
modules/local/cooltools/insulation.nf | 2 +-
modules/local/hicexplorer/hicFindTADs.nf | 2 +-
modules/local/hicexplorer/hicPlotDistVsCounts.nf | 2 +-
modules/local/hicpro/bowtie2_merge.nf | 2 +-
modules/local/hicpro/build_contact_maps.nf | 8 ++++----
modules/local/hicpro/combine_mates.nf | 2 +-
modules/local/hicpro/dnase_mapping_stats.nf | 2 +-
modules/local/hicpro/get_restriction_fragments.nf | 2 +-
modules/local/hicpro/get_valid_interaction.nf | 2 +-
modules/local/hicpro/get_valid_interaction_dnase.nf | 2 +-
modules/local/hicpro/hicpro2pairs.nf | 2 +-
modules/local/hicpro/merge_stats.nf | 2 +-
modules/local/hicpro/merge_valid_interaction.nf | 2 +-
modules/local/hicpro/run_ice.nf | 2 +-
modules/local/hicpro/trim_reads.nf | 2 +-
modules/local/multiqc.nf | 2 +-
modules/local/samplesheet_check.nf | 2 +-
modules/local/split_cooler_dump.nf | 2 +-
19 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index feaa300..873bd24 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS {
conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
- 'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
+ 'biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
input:
tuple val(meta), path(cool), val(resolution)
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 8a9127e..af53529 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION {
conda "bioconda::cooltools=0.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index b6cae33..d86dc83 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -8,7 +8,7 @@ process HIC_FIND_TADS {
conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
- 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+ 'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 3e37d3f..1143a05 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS {
conda "bioconda::hicexplorer=3.7.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(cool)
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index 7a4e96b..64aa6e6 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -5,7 +5,7 @@ process MERGE_BOWTIE2{
conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
- 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+ 'biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(bam1), path(bam2)
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index fd633a9..8ff4540 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -5,15 +5,15 @@ process BUILD_CONTACT_MAPS{
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'quay.io/nfcore/ubuntu:20.04' }"
input:
- tuple val(meta), path(vpairs), val(resolution)
- tuple val(meta2), path(chrsize)
+ tuple val(meta), path(vpairs), val(resolution)
+ tuple val(meta2), path(chrsize)
output:
tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
-
+
script:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index da95be8..b0d828e 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -5,7 +5,7 @@ process COMBINE_MATES {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 64cb079..8e85113 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE {
conda "bioconda::samtools=1.15.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
- 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+ 'biocontainers/samtools:1.15.1--h1170115_0' }"
input:
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index affc2d9..56cd74a 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS {
conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(fasta)
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index cc14837..bebd421 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -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"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
- 'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+ 'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 142d0cb..d62318f 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE {
conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 2ba2a90..eb9b86b 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -5,7 +5,7 @@ process HICPRO2PAIRS {
conda "bioconda::pairix=0.3.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
- 'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
+ 'biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input:
tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index b25dc8a..d9c2aec 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -5,7 +5,7 @@ process MERGE_STATS {
conda "conda-forge::python=3.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), path(fstat)
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 29e568a..6a5c830 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'nfcore/ubuntu:20.04' }"
input:
tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 0a435ed..74c96dc 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -5,7 +5,7 @@ process ICE_NORMALIZATION{
conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
tuple val(meta), val(res), path(rmaps), path(bed)
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 5a96df4..f6d2e90 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -5,7 +5,7 @@ process TRIM_READS {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'nfcore/ubuntu:20.04' }"
input:
tuple val(meta), path(reads)
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 595dc94..6f6bad4 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
conda "bioconda::multiqc=1.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'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:
path multiqc_config
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 1624dfa..096c80b 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
- 'quay.io/biocontainers/python:3.8.3' }"
+ 'biocontainers/python:3.8.3' }"
input:
path samplesheet
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index 8b9e45b..c9dde00 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP {
conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'ubuntu:20.04' }"
+ 'nfcore/ubuntu:20.04' }"
input:
tuple val(meta), path(bedpe)
--
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