From 0fd940bcfe6ae60cf867edcceb31c4261d82054d Mon Sep 17 00:00:00 2001 From: svarona Date: Thu, 2 Nov 2023 10:58:55 +0100 Subject: [PATCH] removed quay.io from main.nf --- modules/local/asciigenome.nf | 2 +- modules/local/collapse_primers.nf | 2 +- modules/local/cutadapt.nf | 2 +- modules/local/ivar_variants_to_vcf.nf | 2 +- modules/local/kraken2_build.nf | 2 +- modules/local/make_bed_mask.nf | 2 +- modules/local/make_variants_long_table.nf | 2 +- modules/local/plot_base_density.nf | 2 +- modules/local/plot_mosdepth_regions.nf | 2 +- modules/local/samplesheet_check.nf | 2 +- modules/local/snpeff_ann.nf | 2 +- modules/local/snpeff_build.nf | 2 +- modules/local/snpsift_extractfields.nf | 2 +- modules/nf-core/abacas/main.nf | 2 +- modules/nf-core/artic/guppyplex/main.nf | 2 +- modules/nf-core/artic/minion/main.nf | 2 +- modules/nf-core/bandage/image/main.nf | 2 +- modules/nf-core/bcftools/consensus/main.nf | 2 +- modules/nf-core/bcftools/filter/main.nf | 2 +- modules/nf-core/bcftools/mpileup/main.nf | 2 +- modules/nf-core/bcftools/norm/main.nf | 2 +- modules/nf-core/bcftools/query/main.nf | 2 +- modules/nf-core/bcftools/sort/main.nf | 2 +- modules/nf-core/bcftools/stats/main.nf | 2 +- modules/nf-core/bedtools/getfasta/main.nf | 2 +- modules/nf-core/bedtools/maskfasta/main.nf | 2 +- modules/nf-core/bedtools/merge/main.nf | 2 +- modules/nf-core/blast/blastn/main.nf | 2 +- modules/nf-core/blast/makeblastdb/main.nf | 2 +- modules/nf-core/bowtie2/align/main.nf | 2 +- modules/nf-core/bowtie2/build/main.nf | 2 +- .../custom-dumpsoftwareversions.diff | 14 -------------- modules/nf-core/custom/getchromsizes/main.nf | 2 +- modules/nf-core/fastp/main.nf | 2 +- modules/nf-core/freyja/boot/main.nf | 2 +- modules/nf-core/freyja/demix/main.nf | 2 +- modules/nf-core/freyja/update/main.nf | 2 +- modules/nf-core/freyja/variants/main.nf | 2 +- modules/nf-core/ivar/consensus/main.nf | 2 +- modules/nf-core/ivar/trim/main.nf | 2 +- modules/nf-core/ivar/variants/main.nf | 2 +- modules/nf-core/kraken2/kraken2/main.nf | 2 +- modules/nf-core/minia/main.nf | 2 +- modules/nf-core/mosdepth/main.nf | 2 +- modules/nf-core/nanoplot/main.nf | 2 +- modules/nf-core/nextclade/datasetget/main.nf | 2 +- modules/nf-core/nextclade/run/main.nf | 2 +- modules/nf-core/pangolin/main.nf | 2 +- .../nf-core/picard/collectmultiplemetrics/main.nf | 2 +- modules/nf-core/picard/markduplicates/main.nf | 2 +- modules/nf-core/plasmidid/main.nf | 2 +- modules/nf-core/pycoqc/main.nf | 2 +- modules/nf-core/quast/main.nf | 2 +- modules/nf-core/samtools/flagstat/main.nf | 2 +- modules/nf-core/samtools/idxstats/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/spades/main.nf | 2 +- modules/nf-core/tabix/bgzip/main.nf | 2 +- modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/unicycler/main.nf | 2 +- modules/nf-core/vcflib/vcfuniq/main.nf | 2 +- 64 files changed, 63 insertions(+), 77 deletions(-) delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff diff --git a/modules/local/asciigenome.nf b/modules/local/asciigenome.nf index adf8cf14..3b71bba4 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' : - 'quay.io/biocontainers/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' }" + 'biocontainers/mulled-v2-093691b47d719890dc19ac0c13c4528e9776897f:27211b8c38006480d69eb1be3ef09a7bf0a49d76-0' }" input: tuple val(meta), path(bam), path(vcf) diff --git a/modules/local/collapse_primers.nf b/modules/local/collapse_primers.nf index 4219b6ae..e400dfb2 100644 --- a/modules/local/collapse_primers.nf +++ b/modules/local/collapse_primers.nf @@ -5,7 +5,7 @@ process COLLAPSE_PRIMERS { conda "conda-forge::python=3.9.5" container "${ 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 index 11c8f6a5..3c4785ed 100644 --- a/modules/local/cutadapt.nf +++ b/modules/local/cutadapt.nf @@ -5,7 +5,7 @@ process CUTADAPT { conda "bioconda::cutadapt=4.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:4.2--py39hbf8eff0_0' : - 'quay.io/biocontainers/cutadapt:4.2--py39hbf8eff0_0' }" + 'biocontainers/cutadapt:4.2--py39hbf8eff0_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/ivar_variants_to_vcf.nf b/modules/local/ivar_variants_to_vcf.nf index e6c88328..abaebdf8 100644 --- a/modules/local/ivar_variants_to_vcf.nf +++ b/modules/local/ivar_variants_to_vcf.nf @@ -4,7 +4,7 @@ process IVAR_VARIANTS_TO_VCF { conda "conda-forge::python=3.9.5 conda-forge::matplotlib=3.5.1 conda-forge::pandas=1.3.5 conda-forge::r-sys=3.4 conda-forge::regex=2021.11.10 conda-forge::scipy=1.7.3 conda-forge::biopython=1.79" container "${ 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 index f1aa6865..94515762 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : - 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" + 'biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" input: val library diff --git a/modules/local/make_bed_mask.nf b/modules/local/make_bed_mask.nf index c8c75bff..b3ca5773 100644 --- a/modules/local/make_bed_mask.nf +++ b/modules/local/make_bed_mask.nf @@ -4,7 +4,7 @@ process MAKE_BED_MASK { conda "conda-forge::python=3.9.5 bioconda::samtools=1.14" container "${ 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 index 1d8b40fc..e0f027f0 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' : - 'quay.io/biocontainers/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' }" + 'biocontainers/mulled-v2-77320db00eefbbf8c599692102c3d387a37ef02a:08144a66f00dc7684fad061f1466033c0176e7ad-0' }" input: path ('bcftools_query/*') diff --git a/modules/local/plot_base_density.nf b/modules/local/plot_base_density.nf index 1932350a..803720e7 100644 --- a/modules/local/plot_base_density.nf +++ b/modules/local/plot_base_density.nf @@ -5,7 +5,7 @@ process PLOT_BASE_DENSITY { conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1 conda-forge::r-viridis=0.5.1 conda-forge::r-tidyverse=1.3.0 bioconda::bioconductor-biostrings=2.58.0 bioconda::bioconductor-complexheatmap=2.6.2" container "${ 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 index 0195549b..2d30cb31 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' : - 'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }" + 'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }" input: path beds diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 0da5f587..aae77403 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.9.5" container "${ 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 index c834c1c5..0794e868 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' : - 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }" + 'biocontainers/snpeff:5.0--hdfd78af_1' }" input: tuple val(meta), path(vcf) diff --git a/modules/local/snpeff_build.nf b/modules/local/snpeff_build.nf index e1ab367f..d47c5887 100644 --- a/modules/local/snpeff_build.nf +++ b/modules/local/snpeff_build.nf @@ -5,7 +5,7 @@ process SNPEFF_BUILD { conda "bioconda::snpeff=5.0" container "${ 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 index 5654e97e..392e73af 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : - 'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }" + 'biocontainers/snpsift:4.3.1t--hdfd78af_3' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf index beabc45b..0c3acca3 100644 --- a/modules/nf-core/abacas/main.nf +++ b/modules/nf-core/abacas/main.nf @@ -5,7 +5,7 @@ process ABACAS { conda "bioconda::abacas=1.3.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : - 'quay.io/biocontainers/abacas:1.3.1--pl526_0' }" + 'biocontainers/abacas:1.3.1--pl526_0' }" input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf index 9be33484..73cd1603 100644 --- a/modules/nf-core/artic/guppyplex/main.nf +++ b/modules/nf-core/artic/guppyplex/main.nf @@ -5,7 +5,7 @@ process ARTIC_GUPPYPLEX { conda "bioconda::artic=1.2.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' : - 'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }" + 'biocontainers/artic:1.2.3--pyhdfd78af_0' }" input: tuple val(meta), path(fastq_dir) diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf index 429a107d..e6d8c401 100644 --- a/modules/nf-core/artic/minion/main.nf +++ b/modules/nf-core/artic/minion/main.nf @@ -5,7 +5,7 @@ process ARTIC_MINION { conda "bioconda::artic=1.2.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' : - 'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }" + 'biocontainers/artic:1.2.3--pyhdfd78af_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bandage/image/main.nf b/modules/nf-core/bandage/image/main.nf index e4da7336..53398ed4 100644 --- a/modules/nf-core/bandage/image/main.nf +++ b/modules/nf-core/bandage/image/main.nf @@ -5,7 +5,7 @@ process BANDAGE_IMAGE { conda "bioconda::bandage=0.8.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2' : - 'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2' }" + 'biocontainers/bandage:0.8.1--hc9558a2_2' }" input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf index a32d94b1..01a0bfec 100644 --- a/modules/nf-core/bcftools/consensus/main.nf +++ b/modules/nf-core/bcftools/consensus/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_CONSENSUS { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 4e02009d..d31ed33f 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_FILTER { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf index c9e42c4d..f5a1c91a 100644 --- a/modules/nf-core/bcftools/mpileup/main.nf +++ b/modules/nf-core/bcftools/mpileup/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_MPILEUP { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(bam), path(intervals) diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 90387d6c..1a5b7e60 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_NORM { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index 5a917b3e..37e75579 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_QUERY { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 9ae3253b..21f65238 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_SORT { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 51e9c91c..ac59f63b 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -5,7 +5,7 @@ process BCFTOOLS_STATS { conda "bioconda::bcftools=1.16" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1': - 'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }" + 'biocontainers/bcftools:1.16--hfe4b78e_1' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 57e7f0de..84adc4c9 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_GETFASTA { conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + 'biocontainers/bedtools:2.30.0--hc088bd4_0' }" input: path bed diff --git a/modules/nf-core/bedtools/maskfasta/main.nf b/modules/nf-core/bedtools/maskfasta/main.nf index a84a23c1..827bc360 100644 --- a/modules/nf-core/bedtools/maskfasta/main.nf +++ b/modules/nf-core/bedtools/maskfasta/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_MASKFASTA { conda "bioconda::bedtools=2.30.0" container "${ 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(bed) diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 21b2e645..3f973239 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_MERGE { conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + 'biocontainers/bedtools:2.30.0--hc088bd4_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf index 5f35422a..9a1f3a55 100644 --- a/modules/nf-core/blast/blastn/main.nf +++ b/modules/nf-core/blast/blastn/main.nf @@ -5,7 +5,7 @@ process BLAST_BLASTN { conda "bioconda::blast=2.13.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' : - 'quay.io/biocontainers/blast:2.13.0--hf3cf87c_0' }" + 'biocontainers/blast:2.13.0--hf3cf87c_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index 62abd813..f5763611 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -5,7 +5,7 @@ process BLAST_MAKEBLASTDB { conda "bioconda::blast=2.13.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' : - 'quay.io/biocontainers/blast:2.13.0--hf3cf87c_0' }" + 'biocontainers/blast:2.13.0--hf3cf87c_0' }" input: path fasta diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 3d851866..311a1505 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_ALIGN { conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' : - 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" + 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" input: tuple val(meta) , path(reads) diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 551893af..566a4acc 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -5,7 +5,7 @@ process BOWTIE2_BUILD { conda "bioconda::bowtie2=2.4.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : - 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" + 'biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff deleted file mode 100644 index 4746ec46..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff +++ /dev/null @@ -1,14 +0,0 @@ -Changes in module 'nf-core/custom/dumpsoftwareversions' ---- modules/nf-core/custom/dumpsoftwareversions/main.nf -+++ modules/nf-core/custom/dumpsoftwareversions/main.nf -@@ -5,7 +5,7 @@ - conda "bioconda::multiqc=1.15" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : -- 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" -+ 'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }" - - input: - path versions - -************************************************************ diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 580f87fe..060a2e88 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 5eeb9b09..2ca2d3ee 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -5,7 +5,7 @@ process FASTP { conda "bioconda::fastp=0.23.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" + 'biocontainers/fastp:0.23.2--h79da9fb_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/freyja/boot/main.nf b/modules/nf-core/freyja/boot/main.nf index 10e39d02..ecc4ce43 100644 --- a/modules/nf-core/freyja/boot/main.nf +++ b/modules/nf-core/freyja/boot/main.nf @@ -5,7 +5,7 @@ process FREYJA_BOOT { conda "bioconda::freyja=1.3.12" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freyja:1.3.12--pyhdfd78af_0': - 'quay.io/biocontainers/freyja:1.3.12--pyhdfd78af_0' }" + 'biocontainers/freyja:1.3.12--pyhdfd78af_0' }" input: tuple val(meta), path(variants), path(depths) diff --git a/modules/nf-core/freyja/demix/main.nf b/modules/nf-core/freyja/demix/main.nf index 6587cb3c..6bd32ca1 100644 --- a/modules/nf-core/freyja/demix/main.nf +++ b/modules/nf-core/freyja/demix/main.nf @@ -5,7 +5,7 @@ process FREYJA_DEMIX { conda "bioconda::freyja=1.3.12" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freyja:1.3.12--pyhdfd78af_0': - 'quay.io/biocontainers/freyja:1.3.12--pyhdfd78af_0' }" + 'biocontainers/freyja:1.3.12--pyhdfd78af_0' }" input: tuple val(meta), path(variants), path(depths) diff --git a/modules/nf-core/freyja/update/main.nf b/modules/nf-core/freyja/update/main.nf index 1711b14c..e4d9d696 100644 --- a/modules/nf-core/freyja/update/main.nf +++ b/modules/nf-core/freyja/update/main.nf @@ -5,7 +5,7 @@ process FREYJA_UPDATE { conda "bioconda::freyja=1.3.12" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freyja:1.3.12--pyhdfd78af_0': - 'quay.io/biocontainers/freyja:1.3.12--pyhdfd78af_0' }" + 'biocontainers/freyja:1.3.12--pyhdfd78af_0' }" input: val db_name diff --git a/modules/nf-core/freyja/variants/main.nf b/modules/nf-core/freyja/variants/main.nf index cdc6d788..9ee685f9 100644 --- a/modules/nf-core/freyja/variants/main.nf +++ b/modules/nf-core/freyja/variants/main.nf @@ -5,7 +5,7 @@ process FREYJA_VARIANTS { conda "bioconda::freyja=1.3.12" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/freyja:1.3.12--pyhdfd78af_0': - 'quay.io/biocontainers/freyja:1.3.12--pyhdfd78af_0' }" + 'biocontainers/freyja:1.3.12--pyhdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 827463dd..1bb68de9 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -5,7 +5,7 @@ process IVAR_CONSENSUS { conda "bioconda::ivar=1.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'quay.io/biocontainers/ivar:1.4--h6b7c446_1' }" + 'biocontainers/ivar:1.4--h6b7c446_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/ivar/trim/main.nf b/modules/nf-core/ivar/trim/main.nf index a7dc404d..b821dcb6 100644 --- a/modules/nf-core/ivar/trim/main.nf +++ b/modules/nf-core/ivar/trim/main.nf @@ -5,7 +5,7 @@ process IVAR_TRIM { conda "bioconda::ivar=1.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'quay.io/biocontainers/ivar:1.4--h6b7c446_1' }" + 'biocontainers/ivar:1.4--h6b7c446_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index ae647f2b..3e42d868 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -5,7 +5,7 @@ process IVAR_VARIANTS { conda "bioconda::ivar=1.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'quay.io/biocontainers/ivar:1.4--h6b7c446_1' }" + 'biocontainers/ivar:1.4--h6b7c446_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf index 5901064e..da8d8c6d 100644 --- a/modules/nf-core/kraken2/kraken2/main.nf +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -5,7 +5,7 @@ process KRAKEN2_KRAKEN2 { conda "bioconda::kraken2=2.1.2 conda-forge::pigz=2.6" container "${ 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: tuple val(meta), path(reads) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index fe242920..9ddddde7 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -5,7 +5,7 @@ process MINIA { conda "bioconda::minia=3.2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : - 'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }" + 'biocontainers/minia:3.2.6--h9a82719_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index be4be831..3682c4e6 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -5,7 +5,7 @@ process MOSDEPTH { conda "bioconda::mosdepth=0.3.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : - 'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}" + 'biocontainers/mosdepth:0.3.3--hdfd78af_1'}" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index ca0d8454..9706bb87 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -5,7 +5,7 @@ process NANOPLOT { conda "bioconda::nanoplot=1.41.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanoplot:1.41.0--pyhdfd78af_0' : - 'quay.io/biocontainers/nanoplot:1.41.0--pyhdfd78af_0' }" + 'biocontainers/nanoplot:1.41.0--pyhdfd78af_0' }" input: tuple val(meta), path(ontfile) diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index ab2e20d3..19c5a26b 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -5,7 +5,7 @@ process NEXTCLADE_DATASETGET { conda "bioconda::nextclade=2.12.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.12.0--h9ee0642_0' : - 'quay.io/biocontainers/nextclade:2.12.0--h9ee0642_0' }" + 'biocontainers/nextclade:2.12.0--h9ee0642_0' }" input: val dataset diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 960892b7..f1ae8d23 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -5,7 +5,7 @@ process NEXTCLADE_RUN { conda "bioconda::nextclade=2.12.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nextclade:2.12.0--h9ee0642_0' : - 'quay.io/biocontainers/nextclade:2.12.0--h9ee0642_0' }" + 'biocontainers/nextclade:2.12.0--h9ee0642_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index e2db37b2..4991981d 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -5,7 +5,7 @@ process PANGOLIN { conda "bioconda::pangolin=4.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pangolin:4.2--pyhdfd78af_1' : - 'quay.io/biocontainers/pangolin:4.2--pyhdfd78af_1' }" + 'biocontainers/pangolin:4.2--pyhdfd78af_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index ed88dbe7..91fe9170 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -5,7 +5,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda "bioconda::picard=3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }" + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta) , path(bam), path(bai) diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 1fe6ee2d..7ba8448f 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -5,7 +5,7 @@ process PICARD_MARKDUPLICATES { conda "bioconda::picard=3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }" + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/plasmidid/main.nf b/modules/nf-core/plasmidid/main.nf index ff7165b1..09311651 100644 --- a/modules/nf-core/plasmidid/main.nf +++ b/modules/nf-core/plasmidid/main.nf @@ -5,7 +5,7 @@ process PLASMIDID { conda "bioconda::plasmidid=1.6.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' : - 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0' }" + 'biocontainers/plasmidid:1.6.5--hdfd78af_0' }" input: tuple val(meta), path(scaffold) diff --git a/modules/nf-core/pycoqc/main.nf b/modules/nf-core/pycoqc/main.nf index 02092a4b..a8c21d2a 100644 --- a/modules/nf-core/pycoqc/main.nf +++ b/modules/nf-core/pycoqc/main.nf @@ -5,7 +5,7 @@ process PYCOQC { conda "bioconda::pycoqc=2.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' : - 'quay.io/biocontainers/pycoqc:2.5.2--py_0' }" + 'biocontainers/pycoqc:2.5.2--py_0' }" input: tuple val(meta), path(summary) diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf index a7f9a4c8..ecfbf406 100644 --- a/modules/nf-core/quast/main.nf +++ b/modules/nf-core/quast/main.nf @@ -4,7 +4,7 @@ process QUAST { conda "bioconda::quast=5.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : - 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }" + 'biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }" input: path consensus diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 2120cd7d..d4359794 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_FLAGSTAT { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a7b87d8b..29eb182e 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_IDXSTATS { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8b95687a..723465e0 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_INDEX { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 84c167cd..aa5a12c3 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_SORT { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 0a2a3640..bfcf4777 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_STATS { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 729c85e5..89d06a2d 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -5,7 +5,7 @@ process SAMTOOLS_VIEW { conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'biocontainers/samtools:1.16.1--h6899075_1' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 2c58069c..e424a182 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -5,7 +5,7 @@ process SPADES { conda "bioconda::spades=3.15.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1' : - 'quay.io/biocontainers/spades:3.15.5--h95f258a_1' }" + 'biocontainers/spades:3.15.5--h95f258a_1' }" input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 6dd4e202..8c47d9e2 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -5,7 +5,7 @@ process TABIX_BGZIP { conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 9a404db9..5bf332ef 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -5,7 +5,7 @@ process TABIX_TABIX { conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(tab) diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf index 8981c433..89a65746 100644 --- a/modules/nf-core/unicycler/main.nf +++ b/modules/nf-core/unicycler/main.nf @@ -5,7 +5,7 @@ process UNICYCLER { conda "bioconda::unicycler=0.4.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : - 'quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3' }" + 'biocontainers/unicycler:0.4.8--py38h8162308_3' }" input: tuple val(meta), path(shortreads), path(longreads) diff --git a/modules/nf-core/vcflib/vcfuniq/main.nf b/modules/nf-core/vcflib/vcfuniq/main.nf index 6b09dc4d..05ba2c00 100644 --- a/modules/nf-core/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/vcflib/vcfuniq/main.nf @@ -6,7 +6,7 @@ process VCFLIB_VCFUNIQ { conda "bioconda::vcflib=1.0.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': - 'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }" + 'biocontainers/vcflib:1.0.3--hecb563c_1' }" input: tuple val(meta), path(vcf), path(tbi)