Merge pull request #111 from nf-core/110-change-modules-with-oras

change oras with https for singularity
nf-core · Dec 3, 2024 · 68b165f · 68b165f
2 parents 66e75a6 + a00e84c
commit 68b165f
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Showing 10 changed files with 26 additions and 19 deletions.
diff --git a/modules.json b/modules.json
@@ -57,7 +57,7 @@
                     },
                     "datavzrd": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "09f36ce2d721684f2883fdde4353c563ea15a48c",
                         "installed_by": ["modules"]
                     },
                     "happy/happy": {

diff --git a/modules/local/create_datavzrd_input/main.nf b/modules/local/create_datavzrd_input/main.nf
@@ -2,6 +2,11 @@ process CREATE_DATAVZRD_INPUT {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::tar=1.34"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'quay.io/nf-core/ubuntu:20.04' }"
+
     input:
     tuple val(meta), path(csv), path(template)
 

diff --git a/modules/local/variant_extractor/main.nf b/modules/local/variant_extractor/main.nf
@@ -4,7 +4,7 @@ process VARIANT_EXTRACTOR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c9964f2ad344f5df543a390ddceb308af0816bed9c9abb9cb400e65525580694/data':
         'community.wave.seqera.io/library/htslib_pysam_tabix_pip_variant-extractor:a12ef217eccf6ba8' }"
 
     input:

diff --git a/modules/local/vcf_to_csv/main.nf b/modules/local/vcf_to_csv/main.nf
@@ -4,7 +4,7 @@ process VCF_TO_CSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pysam_pandas_pip_variant-extractor:a2d9ec4a4efadbc3':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/30/30151e7153f1f845e2723b29048a3cdf842e2dcb1384cfcc86ced0211d5e4895/data':
         'community.wave.seqera.io/library/pysam_pandas_pip_variant-extractor:a2d9ec4a4efadbc3' }"
 
     input:

diff --git a/modules/nf-core/datavzrd/main.nf b/modules/nf-core/datavzrd/main.nf
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -19,11 +19,13 @@ references/rtgtools/genome.sdf/done
 **/summary/datavzrd/**/test/*.{js}
 **/summary/datavzrd/**/test/index_1.html
 **/summary/datavzrd/**/test/data/data_1.js
-**/summary/datavzrd/**/test/plots/*.{js}
-**/summary/datavzrd/**/network/plots/*.{js}
+**/summary/datavzrd/**/test/plots/*.js
+**/summary/datavzrd/**/network/plots/*.js
 **/summary/datavzrd/**/network/*.{js}
 **/summary/datavzrd/**/network/index_1.html
 **/summary/datavzrd/**/network/data/data_1.js
+**/summary/plots/happy/*.png
+**/summary/plots/rtgtools/*.png
 **/summary/plots/**/*.png
 **/summary/comparisons/*.csv
 **/summary/tables/**/*.csv

diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
@@ -229,9 +229,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T13:15:43.288411916"
+        "timestamp": "2024-11-28T16:47:47.024615694"
     },
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": {
         "content": [
@@ -573,8 +573,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T13:13:38.90109915"
+        "timestamp": "2024-11-28T16:45:26.990755841"
     }
 }
diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap
@@ -355,9 +355,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-26T14:01:47.145700457"
+        "timestamp": "2024-11-28T16:51:57.386421371"
     },
     "-stub": {
         "content": [
@@ -654,8 +654,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T12:38:58.811950484"
+        "timestamp": "2024-11-28T16:54:34.483191183"
     }
 }
diff --git a/tests/liftover_hg38.nf.test.snap b/tests/liftover_hg38.nf.test.snap
@@ -349,9 +349,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T13:34:14.298465035"
+        "timestamp": "2024-11-29T09:23:31.648065377"
     },
     "-stub": {
         "content": [

diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
@@ -204,8 +204,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-26T13:55:27.662287528"
+        "timestamp": "2024-11-28T16:58:12.671419675"
     }
 }