Update some module versions (#6798)

* Update modules for versions with ARM builds * update picard containers * Fix containers for getchromsizes * Pick python version with ARM conda builds and biocontainer * Fix other containers * Remove quay.io * Bump bedgraphtobigwig * First batch of nf-test updates * Second batch of nf-test updates * Update thests for liftovervcf * One more nf-test update * Last update: trimgalore * match conda cutadapt to trimgalore container * change r-base for picard * [skip ci] nf-test migration for picard/collectrnaseqmetrics * nf-test migration for picard/filtersamreads * Factor out setup * Move bam checking to nft-bam * Add missing tags
nf-core · Oct 19, 2024 · 49f4e50 · 49f4e50
1 parent 66b2256
commit 49f4e50
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Showing 102 changed files with 850 additions and 611 deletions.
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
@@ -3,5 +3,5 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::htslib=1.20
-  - bioconda::samtools=1.20
+  - bioconda::htslib=1.21
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
+        'biocontainers/samtools:1.21--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
@@ -27,7 +27,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ],
                 "fai": [
                     [
@@ -54,15 +54,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:38:36.927106"
+        "timestamp": "2024-10-18T10:11:37.459094476"
     },
     "test_custom_getchromsizes": {
         "content": [
@@ -87,7 +87,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ],
                 "fai": [
                     [
@@ -109,15 +109,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-20T13:22:34.14237"
+        "timestamp": "2024-10-18T10:11:01.526301351"
     },
     "test_custom_getchromsizes_bgzip": {
         "content": [
@@ -147,7 +147,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ],
                 "fai": [
                     [
@@ -174,15 +174,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-20T13:23:06.241379"
+        "timestamp": "2024-10-18T10:11:14.32456385"
     },
     "test_custom_getchromsizes - stub": {
         "content": [
@@ -207,7 +207,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ],
                 "fai": [
                     [
@@ -229,14 +229,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
+                    "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T12:24:05.697845"
+        "timestamp": "2024-10-18T10:11:26.505487624"
     }
 }
diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python=3.9.5
+  - python=3.10.4
diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_TX2GENE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'biocontainers/python:3.9--1' }"
+        'https://depot.galaxyproject.org/singularity/python:3.10.4' :
+        'biocontainers/python:3.10.4' }"
 
     input:
     tuple val(meta), path(gtf)

diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50"
+                    "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840"
                 ],
                 "tx2gene": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50"
+                    "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-05T13:13:11.305047"
+        "timestamp": "2024-10-18T10:24:12.19104487"
     },
     "saccharomyces_cerevisiae - gtf - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
+                    "versions.yml:md5,48194bffef8cb833e82e31166f3d486c"
                 ],
                 "tx2gene": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
+                    "versions.yml:md5,48194bffef8cb833e82e31166f3d486c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T15:15:34.064489"
+        "timestamp": "2024-10-18T10:24:24.729694098"
     }
 }
diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
+  - bioconda::picard=3.3.0
diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf
@@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap
@@ -3,14 +3,14 @@
         "content": [
             "test.replaced.cram",
             [
-                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
+                "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T09:54:40.471730168"
+        "timestamp": "2024-10-18T10:13:23.115450366"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -30,7 +30,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
+                    "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
                 ],
                 "bai": [
 
@@ -47,28 +47,28 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
+                    "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T09:55:08.402649243"
+        "timestamp": "2024-10-18T10:13:47.23694937"
     },
     "sarscov2 - bam": {
         "content": [
             "null.replaced.bam",
             "null.replaced.bai",
             [
-                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
+                "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T09:54:22.239968953"
+        "timestamp": "2024-10-18T10:12:53.083677142"
     }
 }
diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
+  - bioconda::picard=3.3.0
diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf
@@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bed)

diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+                    "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8"
                 ],
                 "interval_list": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+                    "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-26T10:39:08.82372"
+        "timestamp": "2024-10-18T10:17:35.308452582"
     }
 }
diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
+  - bioconda::picard=3.3.0
diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf
@@ -4,8 +4,8 @@ process PICARD_CLEANSAM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             "798439cbd7fd81cbcc5078022dc5479d",
             [
-                "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22"
+                "versions.yml:md5,412651954aecab12c868ee78cf9fa724"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-26T10:36:05.525364"
+        "timestamp": "2024-10-18T10:46:32.969920917"
     }
 }
diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.2.0
+  - bioconda::picard=3.3.0
diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
-        'biocontainers/picard:3.2.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
+        'biocontainers/picard:3.3.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')