removed quay.io from main.nf

BU-ISCIII · Nov 2, 2023 · 0fd940b · 0fd940b
1 parent 67f531e
commit 0fd940b
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Showing 64 changed files with 63 additions and 77 deletions.
diff --git a/modules/local/asciigenome.nf b/modules/local/asciigenome.nf
@@ -5,7 +5,7 @@ process ASCIIGENOME {
     conda "bioconda::asciigenome=1.16.0 bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' :
-        'quay.io/biocontainers/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' }"
+        'biocontainers/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' }"
 
     input:
     tuple val(meta), path(bam), path(vcf)

diff --git a/modules/local/collapse_primers.nf b/modules/local/collapse_primers.nf
@@ -5,7 +5,7 @@ process COLLAPSE_PRIMERS {
     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 bed

diff --git a/modules/local/cutadapt.nf b/modules/local/cutadapt.nf
@@ -5,7 +5,7 @@ process CUTADAPT {
     conda "bioconda::cutadapt=4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cutadapt:4.2--py39hbf8eff0_0' :
-        'quay.io/biocontainers/cutadapt:4.2--py39hbf8eff0_0' }"
+        'biocontainers/cutadapt:4.2--py39hbf8eff0_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/ivar_variants_to_vcf.nf b/modules/local/ivar_variants_to_vcf.nf
@@ -4,7 +4,7 @@ process IVAR_VARIANTS_TO_VCF {
     conda "conda-forge::python=3.9.5 conda-forge::matplotlib=3.5.1 conda-forge::pandas=1.3.5 conda-forge::r-sys=3.4 conda-forge::regex=2021.11.10 conda-forge::scipy=1.7.3 conda-forge::biopython=1.79"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ff46c3f421ca930fcc54e67ab61c8e1bcbddfe22:1ad3da14f705eb0cdff6b5a44fea4909307524b4-0' :
-        'quay.io/biocontainers/mulled-v2-ff46c3f421ca930fcc54e67ab61c8e1bcbddfe22:1ad3da14f705eb0cdff6b5a44fea4909307524b4-0' }"
+        'biocontainers/mulled-v2-ff46c3f421ca930fcc54e67ab61c8e1bcbddfe22:1ad3da14f705eb0cdff6b5a44fea4909307524b4-0' }"
 
     input:
     tuple val(meta), path(tsv)

diff --git a/modules/local/kraken2_build.nf b/modules/local/kraken2_build.nf
@@ -5,7 +5,7 @@ process KRAKEN2_BUILD {
     conda "bioconda::kraken2=2.1.2 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
-        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
+        'biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
 
     input:
     val library

diff --git a/modules/local/make_bed_mask.nf b/modules/local/make_bed_mask.nf
@@ -4,7 +4,7 @@ process MAKE_BED_MASK {
     conda "conda-forge::python=3.9.5 bioconda::samtools=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a35167f7a491c7086c13835aaa74b39f1f43979:6b5cffa1187cfccf2dc983ed3b5359d49b999eb0-0' :
-        'quay.io/biocontainers/mulled-v2-1a35167f7a491c7086c13835aaa74b39f1f43979:6b5cffa1187cfccf2dc983ed3b5359d49b999eb0-0' }"
+        'biocontainers/mulled-v2-1a35167f7a491c7086c13835aaa74b39f1f43979:6b5cffa1187cfccf2dc983ed3b5359d49b999eb0-0' }"
 
     input:
     tuple val(meta), path(bam), path(vcf)

diff --git a/modules/local/make_variants_long_table.nf b/modules/local/make_variants_long_table.nf
@@ -3,7 +3,7 @@ process MAKE_VARIANTS_LONG_TABLE {
     conda "conda-forge::python=3.9.5 conda-forge::matplotlib=3.5.1 conda-forge::pandas=1.3.5 conda-forge::r-sys=3.4 conda-forge::regex=2021.11.10 conda-forge::scipy=1.7.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' :
-        'quay.io/biocontainers/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' }"
+        'biocontainers/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' }"
 
     input:
     path ('bcftools_query/*')

diff --git a/modules/local/plot_base_density.nf b/modules/local/plot_base_density.nf
@@ -5,7 +5,7 @@ process PLOT_BASE_DENSITY {
     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:
     tuple val(meta), path(fasta)

diff --git a/modules/local/plot_mosdepth_regions.nf b/modules/local/plot_mosdepth_regions.nf
@@ -4,7 +4,7 @@ process PLOT_MOSDEPTH_REGIONS {
     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 beds

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/snpeff_ann.nf b/modules/local/snpeff_ann.nf
@@ -5,7 +5,7 @@ process SNPEFF_ANN {
     conda "bioconda::snpeff=5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
-        'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
+        'biocontainers/snpeff:5.0--hdfd78af_1' }"
 
     input:
     tuple val(meta), path(vcf)

diff --git a/modules/local/snpeff_build.nf b/modules/local/snpeff_build.nf
@@ -5,7 +5,7 @@ process SNPEFF_BUILD {
     conda "bioconda::snpeff=5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
-        'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
+        'biocontainers/snpeff:5.0--hdfd78af_1' }"
 
     input:
     path fasta

diff --git a/modules/local/snpsift_extractfields.nf b/modules/local/snpsift_extractfields.nf
@@ -5,7 +5,7 @@ process SNPSIFT_EXTRACTFIELDS {
     conda "bioconda::snpsift=4.3.1t"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' :
-        'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }"
+        'biocontainers/snpsift:4.3.1t--hdfd78af_3' }"
 
     input:
     tuple val(meta), path(vcf)

diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf
diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf
diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf
diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf
diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf
diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf
diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/freyja/boot/main.nf b/modules/nf-core/freyja/boot/main.nf
diff --git a/modules/nf-core/freyja/demix/main.nf b/modules/nf-core/freyja/demix/main.nf
diff --git a/modules/nf-core/freyja/update/main.nf b/modules/nf-core/freyja/update/main.nf
diff --git a/modules/nf-core/freyja/variants/main.nf b/modules/nf-core/freyja/variants/main.nf
diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf
diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf