Merge branch 'master' into master

nf-core · Feb 27, 2025 · f5377d0 · f5377d0
2 parents 7fec3ac + dd32ce5
commit f5377d0
Show file tree

Hide file tree

Showing 61 changed files with 609 additions and 271 deletions.
diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
@@ -83,13 +83,17 @@
         "subworkflows/nf-core/fastq_align_bwa",
         "subworkflows/nf-core/vcf_annotate_ensemblvep"
     ],
-    "docker_self_hosted": ["modules/nf-core/parabricks"],
+    "docker_self_hosted": [
+        "modules/nf-core/parabricks",
+        "subworkflows/nf-core/deepvariant/tests/equality"
+    ],
     "singularity": [
         "modules/nf-core/bases2fastq",
         "modules/nf-core/deepvariant/rundeepvariant",
         "modules/nf-core/deepvariant/vcfstatsreport",
         "modules/nf-core/deepsomatic",
         "modules/nf-core/parabricks",
-        "modules/nf-core/universc"
+        "modules/nf-core/universc",
+        "subworkflows/nf-core/deepvariant/tests/equality"
     ]
 }
diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml
@@ -4,6 +4,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bbmap=39.01
-  - bioconda::samtools=1.16.1
-  - pigz=2.6
+  - bioconda::bbmap=39.17
+  - bioconda::samtools=1.21
+  - pigz=2.8
diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf
@@ -4,8 +4,8 @@ process BBMAP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' :
-        'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }"
+        'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' :
+        'community.wave.seqera.io/library/bbmap_samtools_pigz:79703e935236b43b' }"
 
     input:
     tuple val(meta), path(fastq)

diff --git a/modules/nf-core/bbmap/align/tests/main.nf.test.snap b/modules/nf-core/bbmap/align/tests/main.nf.test.snap
@@ -6,7 +6,7 @@
                 "c17efa4ccc4e9018090792c71af92660"
             ],
             [
-                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+                "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7"
             ]
         ],
         "meta": {
@@ -22,7 +22,7 @@
                 "88d78879c34214288644aec7ec3cb270"
             ],
             [
-                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+                "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7"
             ]
         ],
         "meta": {
@@ -38,7 +38,7 @@
                 "88d78879c34214288644aec7ec3cb270"
             ],
             [
-                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+                "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7"
             ]
         ],
         "meta": {
@@ -54,7 +54,7 @@
                 "88d78879c34214288644aec7ec3cb270"
             ],
             [
-                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+                "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7"
             ]
         ],
         "meta": {
@@ -70,7 +70,7 @@
                 "d41d8cd98f00b204e9800998ecf8427e"
             ],
             [
-                "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb"
+                "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7"
             ]
         ],
         "meta": {
@@ -79,4 +79,4 @@
         },
         "timestamp": "2025-01-08T21:06:47.377762689"
     }
-}
+}
diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bbmap=39.10
+  - bioconda::bbmap=39.17
diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf
@@ -4,8 +4,8 @@ process BBMAP_BBDUK {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0':
-        'biocontainers/bbmap:39.10--h92535d8_0' }"
+        'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0':
+        'biocontainers/bbmap:39.17--he5f24ec_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                 ]
             ],
             [
-                "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
             ]
         ],
         "meta": {
@@ -26,7 +26,7 @@
     "sarscov2 - single end w/ contams [fastq,fasta] - fastq": {
         "content": [
             [
-                "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
             ]
         ],
         "meta": {
@@ -38,7 +38,7 @@
     "sarscov2 - paired end w/ contams [fastq,fasta] - fastq": {
         "content": [
             [
-                "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
             ]
         ],
         "meta": {
@@ -72,7 +72,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                    "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
                 ],
                 "log": [
                     [
@@ -96,7 +96,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                    "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
                 ]
             }
         ],
@@ -128,7 +128,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                    "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
                 ],
                 "log": [
                     [
@@ -149,7 +149,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                    "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
                 ]
             }
         ],
@@ -171,7 +171,7 @@
                 ]
             ],
             [
-                "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c"
+                "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e"
             ]
         ],
         "meta": {
@@ -180,4 +180,4 @@
         },
         "timestamp": "2024-10-19T15:58:00.420305019"
     }
-}
+}
diff --git a/modules/nf-core/bbmap/bbmerge/environment.yml b/modules/nf-core/bbmap/bbmerge/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bbmap=39.10
+  - bioconda::bbmap=39.17
diff --git a/modules/nf-core/bbmap/bbmerge/main.nf b/modules/nf-core/bbmap/bbmerge/main.nf
@@ -3,8 +3,8 @@ process BBMAP_BBMERGE {
     label 'process_single'
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0':
-        'biocontainers/bbmap:39.10--h92535d8_0' }"
+        'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0':
+        'biocontainers/bbmap:39.17--he5f24ec_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2_illumina_paired - fastq_gz": {
         "content": [
             [
-                "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
             ]
         ],
         "meta": {
@@ -42,7 +42,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                    "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
                 ],
                 "4": [
                     "test.bbmerge.log:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -78,7 +78,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                    "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
                 ]
             }
         ],
@@ -91,7 +91,7 @@
     "sarscov2_illumina_interleaved - fastq_gz": {
         "content": [
             [
-                "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
             ]
         ],
         "meta": {
@@ -134,7 +134,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                    "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
                 ],
                 "4": [
                     "test.bbmerge.log:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -173,7 +173,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2"
+                    "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5"
                 ]
             }
         ],
@@ -183,4 +183,4 @@
         },
         "timestamp": "2024-10-19T16:01:24.272511838"
     }
-}
+}
diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bbmap=39.01
-  - pigz=2.6
+  - bioconda::bbmap=39.17
+  - pigz=2.8
diff --git a/modules/nf-core/bbmap/bbnorm/main.nf b/modules/nf-core/bbmap/bbnorm/main.nf
@@ -4,9 +4,8 @@ process BBMAP_BBNORM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0':
-        'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }"
-
+        'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' :
+        'community.wave.seqera.io/library/bbmap_samtools_pigz:79703e935236b43b' }"
     input:
     tuple val(meta), path(fastq)
 

diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap
@@ -10,7 +10,7 @@
             ],
             "test.bbnorm.log",
             [
-                "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01"
+                "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2"
             ]
         ],
         "meta": {
@@ -30,7 +30,7 @@
             ],
             "test.bbnorm.log",
             [
-                "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01"
+                "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2"
             ]
         ],
         "meta": {
@@ -53,7 +53,7 @@
             ],
             "test.bbnorm.log",
             [
-                "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01"
+                "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2"
             ]
         ],
         "meta": {
@@ -65,11 +65,11 @@
     "test-bbmap-bbnorm-se": {
         "content": [
             [
-                
+
             ],
             "test.bbnorm.log",
             [
-                "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01"
+                "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2"
             ]
         ],
         "meta": {
@@ -78,4 +78,4 @@
         },
         "timestamp": "2024-08-26T14:59:16.676091"
     }
-}
+}
diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bbmap=39.10
+  - bioconda::bbmap=39.17
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -5,8 +5,8 @@ process BBMAP_BBSPLIT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0':
-        'biocontainers/bbmap:39.10--h92535d8_0' }"
+        'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0':
+        'biocontainers/bbmap:39.17--he5f24ec_0' }"
 
     input:
     tuple val(meta), path(reads)