Update mirtop version (#6663)

* update mirtop to 0.4.28 * add prefix to gff outputs * update tests
nf-core · Sep 20, 2024 · 1960623 · 1960623
1 parent 6666521
commit 1960623
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Showing 15 changed files with 114 additions and 77 deletions.
diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml
@@ -4,6 +4,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::mirtop=0.4.25"
-  - "conda-forge::r-base=4.1.1"
-  - "conda-forge::r-data.table=1.14.2"
+  - "bioconda::mirtop=0.4.28"
+  - "bioconda::samtools=1.21"
+  - "conda-forge::python=3.11"
+  - "conda-forge::biopython=1.83"
+  - "bioconda::pysam=0.22.1"
+  - "bioconda::pybedtools=0.10.0"
+  - "conda-forge::pandas=2.2.2"
diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf
@@ -3,9 +3,7 @@ process MIRTOP_COUNTS {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
-        'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
+    container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910"
 
     input:
     tuple val(meta), path(mirtop_gff)

diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test
@@ -54,12 +54,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.versions
-                        ).match()
-                        },
-                // md5sum is not stable, order of elements in column "variant" change
-                { assert file(process.out.tsv[0][1]).readLines().findAll { it.contains("iso-22-I0S21NSLN") }}
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7"
+                    "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8"
                 ],
                 "tsv": [
                     [
@@ -22,26 +22,47 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7"
+                    "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-03T13:24:41.148536938"
+        "timestamp": "2024-09-18T15:05:22.556134542"
     },
     "isomir - bam": {
         "content": [
-            [
-                "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "sample_sim_isomir_bam"
+                        },
+                        "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "sample_sim_isomir_bam"
+                        },
+                        "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-04T18:39:50.607483472"
+        "timestamp": "2024-09-18T16:05:58.332523272"
     }
 }
diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml
@@ -1,10 +1,11 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::mirtop=0.4.25"
-  - "bioconda::samtools=1.15.1"
-  - "conda-forge::r-base=4.1.1"
-  - "conda-forge::r-data.table=1.14.2"
+  - "bioconda::mirtop=0.4.28"
+  - "bioconda::samtools=1.21"
+  - "conda-forge::python=3.11"
+  - "conda-forge::biopython=1.83"
+  - "bioconda::pysam=0.22.1"
+  - "bioconda::pybedtools=0.10.0"
+  - "conda-forge::pandas=2.2.2"
diff --git a/modules/nf-core/mirtop/export/main.nf b/modules/nf-core/mirtop/export/main.nf
@@ -3,9 +3,7 @@ process MIRTOP_EXPORT {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
-        'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
+    container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910"
 
     input:
     tuple val(meta), path(mirtop_gff)

diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c"
+                    "versions.yml:md5,f107a819b949304d703be77d60d97ae9"
                 ],
                 "fasta": [
                     [
@@ -44,15 +44,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c"
+                    "versions.yml:md5,f107a819b949304d703be77d60d97ae9"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-03T15:25:40.531010949"
+        "timestamp": "2024-09-18T14:54:17.653801164"
     },
     "isomir - bam": {
         "content": [
@@ -72,7 +72,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c"
+                    "versions.yml:md5,f107a819b949304d703be77d60d97ae9"
                 ],
                 "fasta": [
 
@@ -89,14 +89,14 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c"
+                    "versions.yml:md5,f107a819b949304d703be77d60d97ae9"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-12T23:12:49.612315132"
+        "timestamp": "2024-09-18T16:06:37.626754369"
     }
 }
diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml
@@ -4,5 +4,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::mirtop=0.4.25"
-  - "bioconda::samtools=1.15.1"
+  - "bioconda::mirtop=0.4.28"
+  - "bioconda::samtools=1.21"
+  - "conda-forge::python=3.11"
+  - "conda-forge::biopython=1.83"
+  - "bioconda::pysam=0.22.1"
+  - "bioconda::pybedtools=0.10.0"
+  - "conda-forge::pandas=2.2.2"
diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf
@@ -3,9 +3,7 @@ process MIRTOP_GFF {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
-        'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
+    container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910"
 
     input:
     tuple val(meta), path(bam, arity:'1..*')
@@ -14,7 +12,7 @@ process MIRTOP_GFF {
 
     output:
     tuple val(meta), path("mirtop/*mirtop.gff")           , emit: gff
-    path "versions.yml"                                  , emit: versions
+    path "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test
@@ -33,13 +33,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.bam,
-                    process.out.versions,
-                        ).match()
-                        },
-                // md5sum is not stable, order of elements in section "variant" may change
-                { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }}
+                { assert snapshot(process.out).match() }
                 )
         }
 

diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
+                    "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314"
                 ],
                 "gff": [
                     [
@@ -22,27 +22,47 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
+                    "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-12T22:40:30.542921953"
+        "timestamp": "2024-09-18T14:31:04.976117723"
     },
     "isomir - bam": {
         "content": [
-            null,
-            [
-                "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "sample_sim_isomir_bam"
+                        },
+                        "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "sample_sim_isomir_bam"
+                        },
+                        "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-12T22:38:09.903017316"
+        "timestamp": "2024-09-18T16:07:04.203181613"
     }
 }
diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml
@@ -4,5 +4,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::mirtop=0.4.25"
-  - "conda-forge::pandas=1.3.5"
+  - "bioconda::mirtop=0.4.28"
+  - "bioconda::samtools=1.21"
+  - "conda-forge::python=3.11"
+  - "conda-forge::biopython=1.83"
+  - "bioconda::pysam=0.22.1"
+  - "bioconda::pybedtools=0.10.0"
+  - "conda-forge::pandas=2.2.2"
diff --git a/modules/nf-core/mirtop/stats/main.nf b/modules/nf-core/mirtop/stats/main.nf
@@ -4,9 +4,7 @@ process MIRTOP_STATS {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
-        'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
+    container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910"
 
     input:
     tuple val(meta), path(mirtop_gff)