Merge pull request #135 from nf-core/134-merge_reports-container-has-…

…high-vulneribilities new container in merge_reports
nf-core · Jan 24, 2025 · c887d26 · c887d26
2 parents f2c6b03 + 009b72e
commit c887d26
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Showing 11 changed files with 41 additions and 41 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -97,7 +97,7 @@ process {
         ext.prefix = {input.baseName - ".vcf" + ".renamechr"}
         ext.args   = {"--output-type z"}
         publishDir = [
-            path: {params.liftover == "truth"? "${params.outdir}/${params.variant_type}/${params.truth_id}/preprocess/liftover" : "${params.outdir}/${params.variant_type}/${meta.id}/preporcess/liftover"},
+            path: {params.liftover == "truth"? "${params.outdir}/${params.variant_type}/${params.truth_id}/preprocess/liftover" : "${params.outdir}/${params.variant_type}/${meta.id}/preprocess/liftover"},
             pattern: "*{.vcf.gz}",
             mode: params.publish_dir_mode
         ]

diff --git a/conf/tests/liftover_test.config b/conf/tests/liftover_test.config
@@ -32,8 +32,8 @@ params {
     min_sv_size          = 30
 
     truth_id             = "HG002"
-    truth_vcf            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg38/truth/HG002_GRCh38_difficult_medical_gene_SV_benchmark_v0.01.chr21.vcf.gz"
-    regions_bed          = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg38/truth/HG002_GRCh38_difficult_medical_gene_SV_benchmark_v01.ch21.bed"
+    truth_vcf            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_SVs_Tier1_v0.6.chr21.vcf.gz"
+    regions_bed          = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_SVs_Tier1_v0.6.chr21.bed"
 
     //liftover files
     liftover              = "test"

diff --git a/modules/local/merge_reports/environment.yml b/modules/local/merge_reports/environment.yml
@@ -1,6 +1,7 @@
-name: merge_reports
 channels:
-  - defaults
+  - conda-forge
+  - bioconda
 dependencies:
-  - python=3.7
-  - pandas=1.3.3
+  - pip
+  - pip:
+      - pandas==2.2.3
diff --git a/modules/local/merge_reports/main.nf b/modules/local/merge_reports/main.nf
@@ -4,8 +4,8 @@ process MERGE_REPORTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0':
-        'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/ab3b0054e3111812d8f2deb12345d5b7ca7ea7b18a2dbcbf174d46274c28deba/data':
+        'community.wave.seqera.io/library/pip_pandas:40d2e76c16c136f0' }"
 
     input:
     tuple val(meta), path(inputs)

diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
@@ -49,7 +49,7 @@
                     "pre.py": "0.3.14"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -242,9 +242,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-16T15:55:45.473583366"
+        "timestamp": "2025-01-23T14:25:38.877918008"
     },
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": {
         "content": [
@@ -296,7 +296,7 @@
                     "pre.py": "0.3.14"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -599,8 +599,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:31:09.115891055"
+        "timestamp": "2025-01-23T14:23:40.862874525"
     }
 }
diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap
@@ -46,7 +46,7 @@
                     "datavzrd": "2.36.12"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -360,9 +360,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:36:16.512872909"
+        "timestamp": "2025-01-23T14:44:34.135136556"
     },
     "-stub": {
         "content": [
@@ -411,7 +411,7 @@
                     "datavzrd": "2.36.12"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -664,8 +664,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-16T15:43:53.130315988"
+        "timestamp": "2025-01-23T14:46:46.270536815"
     }
 }
diff --git a/tests/liftover_test.nf.test.snap b/tests/liftover_test.nf.test.snap
@@ -34,7 +34,7 @@
                     "datavzrd": "2.36.12"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PICARD_CREATESEQUENCEDICTIONARY": {
                     "picard": "3.2.0-1-g3948afb6b"
@@ -196,10 +196,9 @@
                 "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-base.vcf.gz.tbi",
                 "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz",
                 "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz.tbi",
-                "structural/test2/preporcess",
-                "structural/test2/preporcess/liftover",
-                "structural/test2/preporcess/liftover/test2.reformatted.renamechr.vcf.gz",
                 "structural/test2/preprocess",
+                "structural/test2/preprocess/liftover",
+                "structural/test2/preprocess/liftover/test2.reformatted.renamechr.vcf.gz",
                 "structural/test2/preprocess/test2.vcf.gz",
                 "structural/test2/preprocess/test2.vcf.gz.tbi",
                 "structural/test2/stats",
@@ -209,8 +208,8 @@
                 "structural/test2/stats/survivor/test2.manta_mqc.stats"
             ],
             [
-                "HG002.bcftools_stats.txt:md5,142c1fab782c9eb2aa932440e1589461",
-                "HG002_mqc.stats:md5,68681df47b35e3193be03610f5c6e3d6",
+                "HG002.bcftools_stats.txt:md5,f63d8da43be98bae4e02c43966313e5c",
+                "HG002_mqc.stats:md5,ba6a6398a99b95579872576cacde4c8c",
                 "test1.delly.bcftools_stats.txt:md5,f204ab10d82b3cbc9ee51cb6ad548121",
                 "test1.delly_mqc.stats:md5,e140ad55975c767578b0dd6aff58ba29",
                 "test2.manta.bcftools_stats.txt:md5,0de1446278a5448b7dc5a02bcbf927a4",
@@ -219,8 +218,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T10:22:18.275352814"
+        "timestamp": "2025-01-24T08:56:44.966454325"
     }
 }
diff --git a/tests/liftover_truth.nf.test.snap b/tests/liftover_truth.nf.test.snap
@@ -49,7 +49,7 @@
                     "hap.py": "0.3.14"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -361,8 +361,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:02:13.833941457"
+        "timestamp": "2025-01-24T08:45:10.41490994"
     }
 }
diff --git a/tests/somatic_indel.nf.test.snap b/tests/somatic_indel.nf.test.snap
@@ -31,7 +31,7 @@
                     "hap.py": "0.3.14"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -179,8 +179,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:20:01.232442793"
+        "timestamp": "2025-01-23T15:22:31.866027222"
     }
 }
diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap
@@ -31,7 +31,7 @@
                     "hap.py": "0.3.14"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -130,8 +130,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:17:06.41202116"
+        "timestamp": "2025-01-23T15:15:47.829389807"
     }
 }
diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
@@ -43,7 +43,7 @@
                     "datavzrd": "2.36.12"
                 },
                 "MERGE_REPORTS": {
-                    "python": "3.8.6"
+                    "python": "3.13.0"
                 },
                 "PLOTS": {
                     "r-base": "4.3.1"
@@ -216,8 +216,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-17T09:27:15.598502393"
+        "timestamp": "2025-01-23T15:08:15.346103131"
     }
 }