Remove quay.io from biocontainer address

nf-core · Jul 19, 2023 · fa3221e · fa3221e
1 parent 92bc1be
commit fa3221e
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Showing 16 changed files with 18 additions and 16 deletions.
diff --git a/modules/local/bam_remove_orphans.nf b/modules/local/bam_remove_orphans.nf
@@ -8,7 +8,7 @@ process BAM_REMOVE_ORPHANS {
     conda "bioconda::pysam=0.19.0 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' :
-        'quay.io/biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' }"
+        'biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/local/bamtools_filter.nf b/modules/local/bamtools_filter.nf
@@ -5,7 +5,7 @@ process BAMTOOLS_FILTER {
     conda "bioconda::bamtools=2.5.2 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' :
-        'quay.io/biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' }"
+        'biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

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), path(flagstat)

diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
@@ -7,7 +7,7 @@ process DESEQ2_QC {
     conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
-        'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
+        'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
 
     input:
     tuple val(meta), path(counts)

diff --git a/modules/local/frip_score.nf b/modules/local/frip_score.nf
@@ -5,7 +5,7 @@ process FRIP_SCORE {
     conda "bioconda::bedtools=2.30.0 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0':
-        'quay.io/biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0' }"
+        'biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0' }"
 
     input:
     tuple val(meta), path(bam), path(peak)

diff --git a/modules/local/genome_blacklist_regions.nf b/modules/local/genome_blacklist_regions.nf
@@ -7,7 +7,7 @@ process GENOME_BLACKLIST_REGIONS {
     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:
     path sizes

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/igv.nf b/modules/local/igv.nf
@@ -6,7 +6,7 @@ process IGV {
     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:
     val aligner_dir

diff --git a/modules/local/macs2_consensus.nf b/modules/local/macs2_consensus.nf
@@ -8,7 +8,7 @@ process MACS2_CONSENSUS {
     conda "conda-forge::biopython conda-forge::r-optparse=1.7.1 conda-forge::r-upsetr=1.4.0 bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0':
-        'quay.io/biocontainers/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0' }"
+        'biocontainers/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0' }"
 
     input:
     tuple val(meta), path(peaks)

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
     conda "bioconda::multiqc=1.13a"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1':
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
 
     input:
     path multiqc_config

diff --git a/modules/local/multiqc_custom_peaks.nf b/modules/local/multiqc_custom_peaks.nf
@@ -1,9 +1,10 @@
 process MULTIQC_CUSTOM_PEAKS {
     tag "$meta.id"
+
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/library/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(peak), path(frip)
@@ -13,6 +14,7 @@ process MULTIQC_CUSTOM_PEAKS {
     output:
     tuple val(meta), path("*.peak_count_mqc.tsv"), emit: count
     tuple val(meta), path("*.FRiP_mqc.tsv")      , emit: frip
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/multiqc_custom_phantompeakqualtools.nf b/modules/local/multiqc_custom_phantompeakqualtools.nf
@@ -3,7 +3,7 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     conda "conda-forge::r-base=3.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-base:3.5.1':
-        'quay.io/biocontainers/r-base:3.5.1' }"
+        'biocontainers/r-base:3.5.1' }"
 
     input:
     tuple val(meta), path(spp), path(rdata)

diff --git a/modules/local/plot_homer_annotatepeaks.nf b/modules/local/plot_homer_annotatepeaks.nf
@@ -4,7 +4,7 @@ process PLOT_HOMER_ANNOTATEPEAKS {
     conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1 conda-forge::r-viridis=0.5.1 conda-forge::r-tidyverse=1.3.0 bioconda::bioconductor-biostrings=2.58.0 bioconda::bioconductor-complexheatmap=2.6.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0':
-        'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
+        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
 
     input:
     path annos

diff --git a/modules/local/plot_macs2_qc.nf b/modules/local/plot_macs2_qc.nf
@@ -4,7 +4,7 @@ process PLOT_MACS2_QC {
     conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1 conda-forge::r-viridis=0.5.1 conda-forge::r-tidyverse=1.3.0 bioconda::bioconductor-biostrings=2.58.0 bioconda::bioconductor-complexheatmap=2.6.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0':
-        'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
+        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
 
     input:
     path peaks

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -6,7 +6,7 @@ process STAR_ALIGN {
     conda "bioconda::star=2.6.1d"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/star:2.6.1d--0' :
-        'quay.io/biocontainers/star:2.6.1d--0' }"
+        'biocontainers/star:2.6.1d--0' }"
 
     input:
     tuple val(meta) , path(reads)

diff --git a/modules/local/star_genomegenerate.nf b/modules/local/star_genomegenerate.nf
@@ -6,7 +6,7 @@ process STAR_GENOMEGENERATE {
     conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
 
     input:
     path fasta