Merge branch 'fix/language-server' of github.com:nvnieuwk/nf-core-rna…

…var into fix/language-server
nf-core · Jan 10, 2025 · 8164c37 · 8164c37
2 parents 8a69313 + 64950b7
commit 8164c37
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Showing 8 changed files with 53 additions and 53 deletions.
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
@@ -74,7 +74,7 @@ workflow PREPARE_GENOME {
     star_index       = STAR_GENOMEGENERATE.out.index.first()                                //    path: star/index/
     dbsnp_tbi        = TABIX_DBSNP.out.tbi.map{ _meta, tbi -> [tbi] }.collect()              // path: dbsnb.vcf.gz.tbi
     known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect()       // path: {known_indels*}.vcf.gz.tbi
-    versions         = ch_versions                                                          // channel: [ ch_versions.yml ]
+    versions         = ch_versions                                                          // channel: [ versions.yml ]
     // bedtools_sort    = bedtools_sort    // path: sort.bed
     // bedtools_merge   = bedtools_merge   // path: merge.bed
 }
diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap
@@ -257,10 +257,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-09T16:57:22.127665971"
+        "timestamp": "2025-01-09T16:19:12.045032239"
     },
     "Run with profile test | annotation with vep": {
         "content": [

diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap
@@ -28,29 +28,29 @@
                     "gatk4": "4.5.0.0"
                 },
                 "PICARD_MARKDUPLICATES": {
-                    "picard": "3.1.1"
+                    "picard": "3.3.0"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_IDXSTATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_SORT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "STAR_ALIGN": {
-                    "star": "2.7.10a",
-                    "samtools": 1.18,
+                    "star": "2.7.11b",
+                    "samtools": 1.21,
                     "gawk": "5.1.0"
                 },
                 "TABIX": {
@@ -100,9 +100,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-08T14:02:00.162034514"
+        "timestamp": "2025-01-09T16:22:32.936861849"
     }
 }
diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap
@@ -25,13 +25,13 @@
                     "gatk4": "4.5.0.0"
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "TABIX": {
                     "tabix": "1.19.1"
@@ -71,9 +71,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-07T17:03:13.667134079"
+        "timestamp": "2025-01-09T16:24:31.090393575"
     }
 }
diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap
@@ -25,13 +25,13 @@
                     "gatk4": "4.5.0.0"
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "TABIX": {
                     "tabix": "1.19.1"
@@ -71,9 +71,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-07T17:05:36.02051331"
+        "timestamp": "2025-01-09T16:26:33.364598229"
     }
 }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -31,29 +31,29 @@
                     "gatk4": "4.5.0.0"
                 },
                 "PICARD_MARKDUPLICATES": {
-                    "picard": "3.1.1"
+                    "picard": "3.3.0"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_IDXSTATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_SORT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "STAR_ALIGN": {
-                    "star": "2.7.10a",
-                    "samtools": 1.18,
+                    "star": "2.7.11b",
+                    "samtools": 1.21,
                     "gawk": "5.1.0"
                 },
                 "TABIX": {
@@ -105,9 +105,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-08T14:15:23.218615886"
+        "timestamp": "2025-01-09T16:29:28.081229818"
     }
 }
diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap
@@ -31,29 +31,29 @@
                     "gatk4": "4.5.0.0"
                 },
                 "PICARD_MARKDUPLICATES": {
-                    "picard": "3.1.1"
+                    "picard": "3.3.0"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_IDXSTATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_SORT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "STAR_ALIGN": {
-                    "star": "2.7.10a",
-                    "samtools": 1.18,
+                    "star": "2.7.11b",
+                    "samtools": 1.21,
                     "gawk": "5.1.0"
                 },
                 "TABIX": {
@@ -105,9 +105,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-08T14:21:28.482683082"
+        "timestamp": "2025-01-09T16:32:25.501338685"
     }
 }
diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap
@@ -25,29 +25,29 @@
                     "gatk4": "4.5.0.0"
                 },
                 "PICARD_MARKDUPLICATES": {
-                    "picard": "3.1.1"
+                    "picard": "3.3.0"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_IDXSTATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_INDEX": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_MERGE": {
                     "samtools": "1.19.2"
                 },
                 "SAMTOOLS_SORT": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "SAMTOOLS_STATS": {
-                    "samtools": "1.19.2"
+                    "samtools": 1.21
                 },
                 "STAR_ALIGN": {
-                    "star": "2.7.10a",
-                    "samtools": 1.18,
+                    "star": "2.7.11b",
+                    "samtools": 1.21,
                     "gawk": "5.1.0"
                 },
                 "TABIX": {
@@ -97,9 +97,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-08T14:26:44.327045503"
+        "timestamp": "2025-01-09T16:35:18.554293763"
     }
 }