Update all local modules

drpatelh · drpatelh · commit 0a1bdcfbb498 · 2023-05-06T21:09:15.000+01:00
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
@@ -5,7 +5,7 @@ process BEDTOOLS_GENOMECOV {
     conda "bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta.nf
@@ -4,7 +4,7 @@ process CAT_ADDITIONAL_FASTA {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path fasta
diff --git a/modules/local/dupradar.nf b/modules/local/dupradar.nf
@@ -5,7 +5,7 @@ process DUPRADAR {
     conda "bioconda::bioconductor-dupradar=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dupradar:1.28.0--r42hdfd78af_0' :
-        'quay.io/biocontainers/bioconductor-dupradar:1.28.0--r42hdfd78af_0' }"
+        'biocontainers/bioconductor-dupradar:1.28.0--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
@@ -5,7 +5,7 @@ process GTF2BED {
     conda "conda-forge::perl=5.26.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
-        'quay.io/biocontainers/perl:5.26.2' }"
+        'biocontainers/perl:5.26.2' }"
 
     input:
     path gtf
diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter.nf
@@ -4,7 +4,7 @@ process GTF_GENE_FILTER {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path fasta
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
     conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path multiqc_config
diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype.nf
@@ -4,7 +4,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     tuple val(meta), path(count)
diff --git a/modules/local/preprocess_transcripts_fasta_gencode.nf b/modules/local/preprocess_transcripts_fasta_gencode.nf
@@ -4,7 +4,7 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
     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' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path fasta
diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts.nf
@@ -4,7 +4,7 @@ process RSEM_MERGE_COUNTS {
     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' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path ('genes/*')
diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment.nf
@@ -5,7 +5,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
     conda "bioconda::bioconductor-summarizedexperiment=1.24.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.24.0--r41hdfd78af_0' :
-        'quay.io/biocontainers/bioconductor-summarizedexperiment:1.24.0--r41hdfd78af_0' }"
+        'biocontainers/bioconductor-summarizedexperiment:1.24.0--r41hdfd78af_0' }"
 
     input:
     path counts
diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene.nf
@@ -5,7 +5,7 @@ process SALMON_TX2GENE {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path ("salmon/*")
diff --git a/modules/local/salmon_tximport.nf b/modules/local/salmon_tximport.nf
@@ -4,7 +4,7 @@ process SALMON_TXIMPORT {
     conda "bioconda::bioconductor-tximeta=1.12.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-tximeta:1.12.0--r41hdfd78af_0' :
-        'quay.io/biocontainers/bioconductor-tximeta:1.12.0--r41hdfd78af_0' }"
+        'biocontainers/bioconductor-tximeta:1.12.0--r41hdfd78af_0' }"
 
     input:
     path ("salmon/*")
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
     conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'quay.io/biocontainers/python:3.9--1' }"
+        'biocontainers/python:3.9--1' }"
 
     input:
     path samplesheet
diff --git a/modules/local/umitools_prepareforrsem.nf b/modules/local/umitools_prepareforrsem.nf
@@ -5,7 +5,7 @@ process UMITOOLS_PREPAREFORRSEM {
     conda "bioconda::umi_tools=1.1.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' :
-        'quay.io/biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
+        'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }"
 
     input:
     tuple val(meta), path(bam)
