chore: bump picard (#5948)

* bump picard * fix hsmetrics test * fix markduplicates * fix extractfingerprints * fix addorreplacereadgroups * fix crosscheckfingerprints
nf-core · Jul 10, 2024 · 0dee12b · 0dee12b
1 parent 45d482f
commit 0dee12b
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Showing 50 changed files with 159 additions and 599 deletions.
diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
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:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--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:md5,0a6f049f94501dcf23aabfbc0e272891"
+                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T12:05:47.668865"
+        "timestamp": "2024-07-10T09:54:40.471730168"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -30,7 +30,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
                 ],
                 "bai": [
 
@@ -47,28 +47,28 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T10:51:24.530553"
+        "timestamp": "2024-07-10T09:55:08.402649243"
     },
     "sarscov2 - bam": {
         "content": [
             "null.replaced.bam",
             "null.replaced.bai",
             [
-                "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T12:05:29.696728"
+        "timestamp": "2024-07-10T09:54:22.239968953"
     }
 }
diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
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:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bed)

diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
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:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
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:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')

diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -97,7 +97,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -135,7 +135,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -173,7 +173,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },