Updates for container registry

sanger-tol · Sep 12, 2023 · 30dba23 · 30dba23
1 parent fb74d79
commit 30dba23
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Showing 33 changed files with 34 additions and 30 deletions.
diff --git a/conf/github_full.config b/conf/github_full.config
@@ -21,4 +21,5 @@ params {
 
     // Input data
     input       = "${projectDir}/assets/github_testing/TreeValTinyTest.yaml"
+    outdir      = "TinyTest-FULL"
 }
diff --git a/conf/github_rapid.config b/conf/github_rapid.config
@@ -21,4 +21,5 @@ params {
 
     // Input data
     input       = "${projectDir}/assets/github_testing/TreeValTinyTest.yaml"
+    outdir      = "TinyTest-RAPID"
 }
diff --git a/modules/local/assign_ancestral.nf b/modules/local/assign_ancestral.nf
@@ -5,7 +5,7 @@ process ASSIGN_ANCESTRAL {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'biocontainers/pandas:1.5.2' }"
 
     input:
     tuple val(meta), path(comp_location)

diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf
@@ -4,7 +4,7 @@ process BAMTOBED_SORT {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' :
-        'quay.io/biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }"
+        'biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/local/chunkfasta.nf b/modules/local/chunkfasta.nf
@@ -5,7 +5,7 @@ process CHUNKFASTA {
     conda "conda-forge::pyfasta=0.5.2-1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/pyfasta:0.5.2--py_1' :
-    'quay.io/biocontainers/pyfasta:0.5.2--py_1' }"
+    'biocontainers/pyfasta:0.5.2--py_1' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/local/concatblocks.nf b/modules/local/concatblocks.nf
@@ -5,7 +5,7 @@ process CONCATBLOCKS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
             'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-            'ubuntu:20.04' }"
+            'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(mergeblocks)

diff --git a/modules/local/concatmummer.nf b/modules/local/concatmummer.nf
@@ -5,7 +5,7 @@ process CONCATMUMMER {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
             'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-            'ubuntu:20.04' }"
+            'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(coords)

diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
@@ -4,7 +4,7 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' :
-        'quay.io/biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }"
+        'biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }"
 
     input:
     tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(bwaprefix)

diff --git a/modules/local/extract_ancestral.nf b/modules/local/extract_ancestral.nf
@@ -5,7 +5,7 @@ process EXTRACT_ANCESTRAL {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(fulltable)

diff --git a/modules/local/extract_buscogene.nf b/modules/local/extract_buscogene.nf
@@ -5,7 +5,7 @@ process EXTRACT_BUSCOGENE {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
 
     input:

diff --git a/modules/local/extract_cov_iden.nf b/modules/local/extract_cov_iden.nf
@@ -5,7 +5,7 @@ process EXTRACT_COV_IDEN {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

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

diff --git a/modules/local/extract_telo.nf b/modules/local/extract_telo.nf
@@ -5,7 +5,7 @@ process EXTRACT_TELO {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/find_telomere_windows.nf b/modules/local/find_telomere_windows.nf
@@ -6,7 +6,7 @@ process FIND_TELOMERE_WINDOWS {
     container "${ workflow.containerEngine == 'singularity' &&
                     !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/java-jdk:8.0.112--1' :
-        'quay.io/biocontainers/java-jdk:8.0.112--1' }"
+        'biocontainers/java-jdk:8.0.112--1' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/findhalfcoverage.nf b/modules/local/findhalfcoverage.nf
@@ -5,7 +5,7 @@ process FINDHALFCOVERAGE {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(bedfile)

diff --git a/modules/local/gap_length.nf b/modules/local/gap_length.nf
@@ -5,7 +5,7 @@ process GAP_LENGTH {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf
@@ -6,7 +6,7 @@ process GET_LARGEST_SCAFF {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/get_paired_contact_bed.nf b/modules/local/get_paired_contact_bed.nf
@@ -5,7 +5,7 @@ process GET_PAIRED_CONTACT_BED {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/get_synteny_genomes.nf b/modules/local/get_synteny_genomes.nf
@@ -5,7 +5,7 @@ process GET_SYNTENY_GENOMES {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     val ( synteny_path )

diff --git a/modules/local/getminmaxpunches.nf b/modules/local/getminmaxpunches.nf
@@ -5,7 +5,7 @@ process GETMINMAXPUNCHES{
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bedfile)

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

diff --git a/modules/local/juicer_tools_pre.nf b/modules/local/juicer_tools_pre.nf
@@ -8,7 +8,7 @@ process JUICER_TOOLS_PRE {
     container "${ workflow.containerEngine == 'singularity' &&
                     !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/java-jdk:8.0.112--1' :
-        'quay.io/biocontainers/java-jdk:8.0.112--1' }"
+        'biocontainers/java-jdk:8.0.112--1' }"
 
     input:
     tuple val(meta), path(pairs)

diff --git a/modules/local/makecmap_cmap2bed.nf b/modules/local/makecmap_cmap2bed.nf
@@ -5,7 +5,7 @@ process MAKECMAP_CMAP2BED {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(cmap)

diff --git a/modules/local/makecmap_fa2cmapmulticolor.nf b/modules/local/makecmap_fa2cmapmulticolor.nf
@@ -5,7 +5,7 @@ process MAKECMAP_FA2CMAPMULTICOLOR {
     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:
     tuple val(meta), path(fasta)

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

diff --git a/modules/local/reformat_intersect.nf b/modules/local/reformat_intersect.nf
@@ -5,7 +5,7 @@ process REFORMAT_INTERSECT {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/rename_ids.nf b/modules/local/rename_ids.nf
@@ -5,7 +5,7 @@ process RENAME_IDS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/replace_dots.nf b/modules/local/replace_dots.nf
@@ -5,7 +5,7 @@ process REPLACE_DOTS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/selfcomp_alignmentblocks.nf b/modules/local/selfcomp_alignmentblocks.nf
@@ -5,7 +5,7 @@ process SELFCOMP_ALIGNMENTBLOCKS {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-548f120dc8914d802c46e110ec27751bc1c5a414:8770fa59aa0ae8b50cbf444255b91c201c883685-0' :
-        'quay.io/biocontainers/mulled-v2-548f120dc8914d802c46e110ec27751bc1c5a414:8770fa59aa0ae8b50cbf444255b91c201c883685-0' }"
+        'biocontainers/mulled-v2-548f120dc8914d802c46e110ec27751bc1c5a414:8770fa59aa0ae8b50cbf444255b91c201c883685-0' }"
 
     input:
     tuple val(meta), path(bedfile)

diff --git a/modules/local/selfcomp_mapids.nf b/modules/local/selfcomp_mapids.nf
@@ -5,7 +5,7 @@ process SELFCOMP_MAPIDS {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(bed)

diff --git a/modules/local/selfcomp_mummer2bed.nf b/modules/local/selfcomp_mummer2bed.nf
@@ -5,7 +5,7 @@ process SELFCOMP_MUMMER2BED {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(mummerfile)

diff --git a/modules/local/selfcomp_splitfasta.nf b/modules/local/selfcomp_splitfasta.nf
@@ -5,7 +5,7 @@ process SELFCOMP_SPLITFASTA {
     conda "conda-forge::perl-bioperl=1.7.8-1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
-        'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
+        'biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/nextflow.config b/nextflow.config
@@ -155,6 +155,8 @@ profiles {
     farm_rapid              {   includeConfig 'conf/farm_rapid.config'        }
     github_full             {   includeConfig 'conf/github_full.config'       }
     github_rapid            {   includeConfig 'conf/github_rapid.config'      }
+    local_github_full       {   includeConfig 'conf/local_github_full.config' }
+    local_github_rapid      {   includeConfig 'conf/local_github_rapid.config'}
 }