bump ALL gatk4 modules (#6917)

* bump gatk4 * fix some tests * more tests * more tests * linting * linting * migrate gatk4/createsomaticpanelofnormals to nf-test * migrate printsvevidence * migrate intervallisttobed * migrate filtervarianttranches * migrate sitedepthtobaf * migrate germlinecnvcaller - intermediate commit * ben made me do it * migrate createreadcountpanelofnormals * more nf-test * more nf-test * fix sitedepthtobaf * fix germlinecnvcaller * fix postprocessgermlinecnvcalls linting * fix mergevcfs linting * revert biocontainer for determinegermlinecontigploidy * linting * fix estimatelibrarycomplexity tests * fix splitncigarreads tests * linting * set compiledir for pytorch * linting * linting * fix container definition * are we there yet? * ci: Only run if the PR is from the main repo https://github.com/orgs/community/discussions/26829#discussioncomment-3253575 * apply yaml schema and renovate comments to environment.yml * fix determinegermlinecontigploidy config * chore: Add renovate comments to bowtie2 for sanity check * style: Somehow fix the prettier linting error? * fix whitespace error * linting * Update modules/nf-core/gatk4/cnnscorevariants/environment.yml * Revert "chore: Add renovate comments to bowtie2 for sanity check" This reverts commit dafbfe9. * try to fix tests * add gcnvkernel to conda env * Move to wave containers * Update modules/nf-core/gatk4/printsvevidence/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/gatk4/cnnscorevariants/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/gatk4/createreadcountpanelofnormals/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/gatk4/printsvevidence/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * enable conda tests for gatk4 * drop params.test_data * fix test_data_base * fix createreadcountpanelofnormals snap * fix printsvevidence snap * fix determinegermlinecontigploidy test * fix? * thank you Sateesh * fix cnnscorevariants * fix another one * Delete .github/workflows/test.yml * further enable conda * lower resource labels since gatk is single core at best --------- Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
nf-core · Nov 19, 2024 · 1999eff · 1999eff
1 parent 2a1ee18
commit 1999eff
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diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf
@@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap
@@ -32,7 +32,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
+                    "versions.yml:md5,09f498302943b70029a56ddf65522814"
                 ],
                 "bai": [
                     [
@@ -54,27 +54,27 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
+                    "versions.yml:md5,09f498302943b70029a56ddf65522814"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-03-20T13:19:33.815262"
+        "timestamp": "2024-10-31T10:28:22.832793576"
     },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
+                "versions.yml:md5,09f498302943b70029a56ddf65522814"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-03-20T13:19:18.103325"
+        "timestamp": "2024-10-31T10:28:10.146204216"
     },
     "cram_name": {
         "content": [

diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf
@@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
 
     input:
     tuple val(meta), path(intervals)

diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ],
                 "annotated_intervals": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:07:36.32193"
+        "timestamp": "2024-10-31T10:29:29.006068994"
     },
     "homo_sapiens genome [interval_list]": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ],
                 "annotated_intervals": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:08:12.533176"
+        "timestamp": "2024-10-31T10:30:08.763305448"
     },
     "homo_sapiens genome multi-interval [bed]": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ],
                 "annotated_intervals": [
                     [
@@ -94,15 +94,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:07:54.643276"
+        "timestamp": "2024-10-31T10:29:48.403638052"
     },
     "homo_sapiens genome [interval_list] mappable_regions": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ],
                 "annotated_intervals": [
                     [
@@ -129,28 +129,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:08:31.311782"
+        "timestamp": "2024-10-31T10:30:23.256626974"
     },
     "homo_sapiens genome [bed] - stub": {
         "content": [
             [
                 "test.tsv",
-                "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:09:04.54745"
+        "timestamp": "2024-10-31T10:30:52.179735439"
     },
     "homo_sapiens genome [interval_list] duplication_regions": {
         "content": [
@@ -165,7 +165,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ],
                 "annotated_intervals": [
                     [
@@ -177,14 +177,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
+                    "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-02-13T16:08:49.684766"
+        "timestamp": "2024-10-31T10:30:37.398809104"
     }
 }
diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gatk4=4.5.0.0
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  # renovate: datasource=conda depName=bioconda/gcnvkernel
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf
@@ -4,8 +4,8 @@ process GATK4_APPLYBQSR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)