bump samtools (nf-core#6648)

* bump samtools * samtools cat no longer supports * update snapshots * more snapshots * fix consensus test * another attempt at fixing 'consensus' * reheader > nf-test * markdup > nf-test * fix linting for markdup * consensus fix? * fix consensus --------- Co-authored-by: Sateesh_Peri <[email protected]>
herpov · Oct 2, 2024 · db20e98 · db20e98
1 parent 30b738a
commit db20e98
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diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::samtools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_AMPLICONCLIP {
 
     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(bam)

diff --git a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap
@@ -1,75 +1,45 @@
 {
-    "bam_bed_versions": {
-        "content": [
-            [
-                "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-28T15:43:25.843761003"
-    },
-    "bam_bed_stats": {
+    "bam_bed_save_all_versions": {
         "content": [
             [
-
+                "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-02T13:43:02.239309"
+        "timestamp": "2024-09-16T07:45:31.382344883"
     },
-    "bam_bed_save_all_stats": {
+    "bam_bed_save_all_rejects_bam": {
         "content": [
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a"
+                    "test.cliprejects.bam:md5,8aa0f82e1c2dbfd9fcfab0fe3efa0ada"
                 ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-02T13:43:14.110481"
+        "timestamp": "2024-09-16T07:45:31.334527155"
     },
-    "bam_bed_save_all_versions": {
+    "bam_bed_versions": {
         "content": [
             [
-                "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
+                "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:36.405710677"
-    },
-    "bam_bed_save_all_rejects_bam": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.cliprejects.bam:md5,e3c76daf46d83b2327a1168170b08fca"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-28T15:43:36.39935122"
+        "timestamp": "2024-09-16T07:45:11.300085385"
     },
     "bam_bed_save_clipsats_name": {
         "content": [
@@ -99,15 +69,27 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.cliprejects.bam:md5,f29869fea697a5041f588970d9cf2392"
+                    "test.cliprejects.bam:md5,9d0caf53bd9a8ccb4a5ce60393635ee0"
                 ]
             ]
         ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T07:45:21.573836864"
+    },
+    "bam_bed_stats": {
+        "content": [
+            [
+
+            ]
+        ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "23.04.3"
         },
-        "timestamp": "2024-05-28T15:43:31.133760457"
+        "timestamp": "2024-02-02T13:43:02.239309"
     },
     "bam_bed_save_clipsats_stats": {
         "content": [
@@ -121,17 +103,35 @@
         },
         "timestamp": "2024-02-13T16:13:25.207756781"
     },
-    "bam_bed_save_clipsats_versions": {
+    "bam_bed_save_all_stats": {
         "content": [
             [
-                "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a"
+                ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-02T13:43:14.110481"
+    },
+    "bam_bed_save_clipsats_versions": {
+        "content": [
+            [
+                "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:31.138774495"
+        "timestamp": "2024-09-16T07:45:21.620404522"
     },
     "bam_bed_save_all_name": {
         "content": [

diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::samtools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ {
 
     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(inputbam)

diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
@@ -51,25 +51,25 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
+                "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:52.415053401"
+        "timestamp": "2024-09-16T07:46:07.695175929"
     },
     "bam_split_versions": {
         "content": [
             [
-                "versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
+                "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:43:57.740193087"
+        "timestamp": "2024-09-16T07:46:17.91793415"
     }
 }
diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::samtools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/samtools/calmd/main.nf b/modules/nf-core/samtools/calmd/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_CALMD {
 
     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(bam)

diff --git a/modules/nf-core/samtools/calmd/tests/main.nf.test.snap b/modules/nf-core/samtools/calmd/tests/main.nf.test.snap
@@ -22,25 +22,25 @@
     "bam_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd"
+                "versions.yml:md5,6082f9d3311ea0138839acc5341c115f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:47.344537089"
+        "timestamp": "2024-09-16T07:47:04.212973938"
     },
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd"
+                "versions.yml:md5,6082f9d3311ea0138839acc5341c115f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:42:41.963108136"
+        "timestamp": "2024-09-16T07:46:53.00613089"
     }
 }
diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::samtools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/samtools/cat/main.nf b/modules/nf-core/samtools/cat/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_CAT {
 
     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(input_files, stageAs: "?/*")
@@ -26,7 +26,6 @@ process SAMTOOLS_CAT {
     """
     samtools \\
         cat \\
-        --threads ${task.cpus-1} \\
         $args \\
         -o ${prefix}.${file_type} \\
         $input_files

diff --git a/modules/nf-core/samtools/cat/tests/main.nf.test.snap b/modules/nf-core/samtools/cat/tests/main.nf.test.snap
@@ -14,14 +14,14 @@
     "bams_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8"
+                "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:35.044644556"
+        "timestamp": "2024-09-16T07:47:51.511914861"
     },
     "bams_bam": {
         "content": [
@@ -58,13 +58,13 @@
     "bams_versions": {
         "content": [
             [
-                "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8"
+                "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-28T15:45:29.652817652"
+        "timestamp": "2024-09-16T08:47:50.783194958"
     }
 }
diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  - bioconda::samtools=1.21
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_COLLATE {
 
     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(input)