bump htslib pins for ensemblvep (#11771)

matthdsm · web-flow · commit 251885fdb29e · 2026-05-27T10:07:03.000+02:00
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
@@ -4,5 +4,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # renovate: datasource=conda depName=bioconda/ensembl-vep
   - bioconda::ensembl-vep=115.2
+  # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.23.1
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}"
 
     input:
     tuple val(meta), val(assembly), val(species), val(cache_version)
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
@@ -151,11 +151,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-02-13T13:36:59.060515944",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "26.01.1"
-        },
-        "timestamp": "2026-02-13T13:36:59.060515944"
+        }
     },
     "ENSEMBLVEP download cache for 115_WBcel235 - stub": {
         "content": [
@@ -166,7 +166,7 @@
                             "id": "115_WBcel235"
                         },
                         [
-
+                            
                         ]
                     ]
                 ],
@@ -186,10 +186,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-02-13T13:37:10.696285488",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "26.01.1"
-        },
-        "timestamp": "2026-02-13T13:37:10.696285488"
+        }
     }
 }
diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml
@@ -4,5 +4,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # renovate: datasource=conda depName=bioconda/ensembl-vep
   - bioconda::ensembl-vep=115.2
+  # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.23.1
diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -4,6 +4,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # renovate: datasource=conda depName=bioconda/ensembl-vep
   - bioconda::ensembl-vep=115.2
+  # renovate: datasource=conda depName=bioconda/perl-math-cdf
   - bioconda::perl-math-cdf=0.1
-  - bioconda::htslib=1.21
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.23.1
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data'
-        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/edd02dfaf968d06c808e3c208d5b3e86afb4259590bfa6e5499965ef3bc81881/data'
+        : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf_htslib:efd9a6d1c5f218a9'}"
 
     input:
     tuple val(meta), path(vcf), path(custom_extra_files)
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
@@ -21,15 +21,15 @@
                     [
                         "ENSEMBLVEP_VEP",
                         "tabix",
-                        "1.21"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-06T12:47:57.03116265",
+        "timestamp": "2026-05-27T09:34:16.339141",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.2"
         }
     },
     "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": {
@@ -55,15 +55,15 @@
                     [
                         "ENSEMBLVEP_VEP",
                         "tabix",
-                        "1.21"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-06T12:47:34.421995264",
+        "timestamp": "2026-05-27T09:33:53.016807",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.2"
         }
     }
 }
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap
@@ -21,11 +21,11 @@
                 ]
             ]
         ],
+        "timestamp": "2026-01-20T10:44:55.042159577",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-20T10:44:55.042159577"
+        }
     },
     "WBcel235 caenorhabditis_elegans 115 - test.vcf.gz - stub": {
         "content": [
@@ -49,10 +49,10 @@
                 ]
             ]
         ],
+        "timestamp": "2026-01-20T10:45:05.801478657",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-20T10:45:05.801478657"
+        }
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -151,11 +151,11 @@`
`151`	`151`	`]`
`152`	`152`	`}`
`153`	`153`	`],`
	`154`	`+ "timestamp": "2026-02-13T13:36:59.060515944",`
`154`	`155`	`"meta": {`
`155`	`156`	`"nf-test": "0.9.4",`
`156`	`157`	`"nextflow": "26.01.1"`
`157`		`- },`
`158`		`- "timestamp": "2026-02-13T13:36:59.060515944"`
	`158`	`+ }`
`159`	`159`	`},`
`160`	`160`	`"ENSEMBLVEP download cache for 115_WBcel235 - stub": {`
`161`	`161`	`"content": [`
`@@ -166,7 +166,7 @@`
`166`	`166`	`"id": "115_WBcel235"`
`167`	`167`	`},`
`168`	`168`	`[`
`169`		`-`
	`169`	`+`
`170`	`170`	`]`
`171`	`171`	`]`
`172`	`172`	`],`
`@@ -186,10 +186,10 @@`
`186`	`186`	`]`
`187`	`187`	`}`
`188`	`188`	`],`
	`189`	`+ "timestamp": "2026-02-13T13:37:10.696285488",`
`189`	`190`	`"meta": {`
`190`	`191`	`"nf-test": "0.9.4",`
`191`	`192`	`"nextflow": "26.01.1"`
`192`		`- },`
`193`		`- "timestamp": "2026-02-13T13:37:10.696285488"`
	`193`	`+ }`
`194`	`194`	`}`
`195`	`195`	`}`
Original file line number	Diff line number	Diff line change
`@@ -21,15 +21,15 @@`
`21`	`21`	`[`
`22`	`22`	`"ENSEMBLVEP_VEP",`
`23`	`23`	`"tabix",`
`24`		`- "1.21"`
	`24`	`+ "1.23.1"`
`25`	`25`	`]`
`26`	`26`	`]`
`27`	`27`	`}`
`28`	`28`	`],`
`29`		`- "timestamp": "2026-02-06T12:47:57.03116265",`
	`29`	`+ "timestamp": "2026-05-27T09:34:16.339141",`
`30`	`30`	`"meta": {`
`31`		`- "nf-test": "0.9.3",`
`32`		`- "nextflow": "25.10.3"`
	`31`	`+ "nf-test": "0.9.5",`
	`32`	`+ "nextflow": "26.04.2"`
`33`	`33`	`}`
`34`	`34`	`},`
`35`	`35`	`"test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": {`
`@@ -55,15 +55,15 @@`
`55`	`55`	`[`
`56`	`56`	`"ENSEMBLVEP_VEP",`
`57`	`57`	`"tabix",`
`58`		`- "1.21"`
	`58`	`+ "1.23.1"`
`59`	`59`	`]`
`60`	`60`	`]`
`61`	`61`	`}`
`62`	`62`	`],`
`63`		`- "timestamp": "2026-02-06T12:47:34.421995264",`
	`63`	`+ "timestamp": "2026-05-27T09:33:53.016807",`
`64`	`64`	`"meta": {`
`65`		`- "nf-test": "0.9.3",`
`66`		`- "nextflow": "25.10.3"`
	`65`	`+ "nf-test": "0.9.5",`
	`66`	`+ "nextflow": "26.04.2"`
`67`	`67`	`}`
`68`	`68`	`}`
`69`	`69`	`}`
Original file line number	Diff line number	Diff line change
`@@ -21,11 +21,11 @@`
`21`	`21`	`]`
`22`	`22`	`]`
`23`	`23`	`],`
	`24`	`+ "timestamp": "2026-01-20T10:44:55.042159577",`
`24`	`25`	`"meta": {`
`25`	`26`	`"nf-test": "0.9.3",`
`26`	`27`	`"nextflow": "25.10.2"`
`27`		`- },`
`28`		`- "timestamp": "2026-01-20T10:44:55.042159577"`
	`28`	`+ }`
`29`	`29`	`},`
`30`	`30`	`"WBcel235 caenorhabditis_elegans 115 - test.vcf.gz - stub": {`
`31`	`31`	`"content": [`
`@@ -49,10 +49,10 @@`
`49`	`49`	`]`
`50`	`50`	`]`
`51`	`51`	`],`
	`52`	`+ "timestamp": "2026-01-20T10:45:05.801478657",`
`52`	`53`	`"meta": {`
`53`	`54`	`"nf-test": "0.9.3",`
`54`	`55`	`"nextflow": "25.10.2"`
`55`		`- },`
`56`		`- "timestamp": "2026-01-20T10:45:05.801478657"`
	`56`	`+ }`
`57`	`57`	`}`
`58`	`58`	`}`