nf-core · LeonHafner · Jan 8, 2025 · Dec 21, 2024 · Dec 21, 2024 · Dec 21, 2024
diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)

diff --git a/modules/nf-core/annotsv/installannotations/main.nf b/modules/nf-core/annotsv/installannotations/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations

diff --git a/modules/nf-core/dysgu/environment.yml b/modules/nf-core/dysgu/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - dysgu
+  - dysgu=1.6.5
diff --git a/modules/nf-core/dysgu/main.nf b/modules/nf-core/dysgu/main.nf
@@ -4,8 +4,8 @@ process DYSGU {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/dysgu:48830f55112c399e':
-        'community.wave.seqera.io/library/dysgu:faf71ac972284412' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a8406b0443d7ed75cd1ff9a687b2f7dd6d30e5ce91d79a8e3c9372bebab5e19/data':
+        'community.wave.seqera.io/library/dysgu:1.6.5--69cfa1b1db5c2aec' }"
 
     input:
     tuple val(meta), path(input), path(index)

diff --git a/modules/nf-core/eido/convert/environment.yml b/modules/nf-core/eido/convert/environment.yml
@@ -4,3 +4,4 @@ channels:
 dependencies:
   - conda-forge::eido=0.2.2
   - conda-forge::peppy=0.35.7
+  - conda-forge::setuptools=72.2.0
diff --git a/modules/nf-core/eido/convert/main.nf b/modules/nf-core/eido/convert/main.nf
@@ -4,8 +4,8 @@ process EIDO_CONVERT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/eido_peppy:7f50d6891ca1a6d9' :
-        'community.wave.seqera.io/library/eido_peppy:0de9533940828c4d' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4aef51a3d75d6b950bb643ed5ebc1d7243d67bbf3de0410fcaa7d347e8fc0007/data' :
+        'community.wave.seqera.io/library/eido_peppy_setuptools:53ed68799568c4fa' }"
 
     input:
     path samplesheet

diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf
@@ -4,7 +4,7 @@ process FOLDMASON_EASYMSA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03':
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/067e6389ab95497b753ba1deabaa6acbce25b99c8cfcf39c06d5c1af42fd7751/data':
             'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }"
 
 

diff --git a/modules/nf-core/purecn/intervalfile/main.nf b/modules/nf-core/purecn/intervalfile/main.nf
@@ -4,8 +4,8 @@ process PURECN_INTERVALFILE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:c04754ed02eb7cd3':
-        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:cd51f6d3c90eb24f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31bad5bbf2277cc9ea746c3c4fd440d1689dd7c8d32d0697b5077f08c084a03e/data':
+        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:bc942848b4c78040' }"
 
     input:
     tuple val(meta), path(target_bed)

diff --git a/modules/nf-core/purecn/normaldb/main.nf b/modules/nf-core/purecn/normaldb/main.nf
@@ -4,8 +4,8 @@ process PURECN_NORMALDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:c04754ed02eb7cd3':
-        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:cd51f6d3c90eb24f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31bad5bbf2277cc9ea746c3c4fd440d1689dd7c8d32d0697b5077f08c084a03e/data':
+        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:bc942848b4c78040' }"
 
     input:
     tuple val(meta), path(coverage_files), path(normal_vcf), path(normal_vcf_tbi)

diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf
@@ -4,8 +4,8 @@ process SAMSHEE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pip_samshee:6ef3bad21377d60e' :
-        'community.wave.seqera.io/library/pip_samshee:9a11bec0d7c8df27' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3afa0f69cc7ab7e3f9a80582958b8fa33d6673cb914e0f5bdc1c883f61e16073/data' :
+        'community.wave.seqera.io/library/samshee_python:96db61572eca797e' }"
 
     input:
     tuple val(meta), path(samplesheet)

diff --git a/modules/nf-core/scvitools/scar/environment.yml b/modules/nf-core/scvitools/scar/environment.yml
@@ -1,6 +1,8 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - conda-forge::scvi-tools=1.2.0
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::python=3.12.7
+  - conda-forge::scvi-tools=1.2.0
diff --git a/modules/nf-core/scvitools/scar/main.nf b/modules/nf-core/scvitools/scar/main.nf
@@ -4,7 +4,7 @@ process SCVITOOLS_SCAR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/scvi-tools:1.2.0--adbeb4160de8b08e':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b999caba5a5a6bc19bd324d9f1ac28e092a750140b453071956ebc304b7c4aa/data':
         'community.wave.seqera.io/library/scvi-tools:1.2.0--680d378b86801b8a' }"
 
     input:

diff --git a/modules/nf-core/scvitools/solo/environment.yml b/modules/nf-core/scvitools/solo/environment.yml
@@ -1,6 +1,9 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - conda-forge::scvi-tools=1.2.0
+  - conda-forge::anndata=0.10.9
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::python=3.12.7
+  - conda-forge::scvi-tools=1.2.0
diff --git a/modules/nf-core/scvitools/solo/main.nf b/modules/nf-core/scvitools/solo/main.nf
@@ -6,7 +6,7 @@ process SCVITOOLS_SOLO {
     conda "${moduleDir}/environment.yml"
     container "${ task.ext.use_gpu ? 'docker.io/nicotru/scvitools-gpu:cuda-12' :
         workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/scvi-tools:1.2.0--adbeb4160de8b08e':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b999caba5a5a6bc19bd324d9f1ac28e092a750140b453071956ebc304b7c4aa/data':
         'community.wave.seqera.io/library/scvi-tools:1.2.0--680d378b86801b8a' }"
 
     input:

diff --git a/modules/nf-core/sequali/main.nf b/modules/nf-core/sequali/main.nf
@@ -4,7 +4,7 @@ process SEQUALI {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sequali:0.12.0--c288fa2befb47d0f':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ed3be5b0d3beb64807ec93b25a80b55abdcdffe684114d12ddef78461dd64e9/data':
         'community.wave.seqera.io/library/sequali:0.12.0--07485bec824d914a' }"
 
     input:

diff --git a/modules/nf-core/tcoffee/consensus/main.nf b/modules/nf-core/tcoffee/consensus/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_CONSENSUS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/t-coffee_pigz:f47b85d70360f1a0':
-        'community.wave.seqera.io/library/t-coffee_pigz:6c9b2f8b97ee55e5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5e/5e5c1c07cc0099dacea172348bc78f9a9baab592ce3ece89873703b9e963d269/data':
+        'community.wave.seqera.io/library/t-coffee_pigz:c98a6c87c62d9df6' }"
 
 
     input:

diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf
@@ -10,8 +10,8 @@ process UNTARFILES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/grep_sed_tar:40b34489f8e82876' :
-        'community.wave.seqera.io/library/grep_sed_tar:16f6591cd62505b3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/88e03525287eaeb8bb74114aaee2c67118c1cdcfb99ee52e3ddc71a1acce35d4/data' :
+        'community.wave.seqera.io/library/grep_sed_tar:db2951cd23a1ffde' }"
 
     input:
     tuple val(meta), path(archive)

diff --git a/modules/nf-core/upp/align/main.nf b/modules/nf-core/upp/align/main.nf
@@ -4,8 +4,8 @@ process UPP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sepp_pigz:d72591720d0277b1':
-        'community.wave.seqera.io/library/sepp_pigz:ea6dbc7704a2e251' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/800667a716528cc6d655da1885d38f9d10385a184e0b1165985ae12034ff5f1d/data':
+        'community.wave.seqera.io/library/sepp_pigz:8f996974b960fc41' }"
 
     input:
     tuple val(meta) , path(fasta)