Merge pull request #173 from nf-core/fix-config-selectors

nf-core · Dec 21, 2024 · 7425043 · 7425043
2 parents 2d19d95 + 723e873
commit 7425043
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Showing 6 changed files with 14 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#171](https://github.com/nf-core/nascent/pull/171) - Clean up MultiQC report
 - [#170](https://github.com/nf-core/nascent/pull/170) - Remove "Access to undefined parameter forwardStranded" warnings
+- [#173](https://github.com/nf-core/nascent/pull/173) - Fix config selectors
+- [#173](https://github.com/nf-core/nascent/pull/173) - Remove STAR transcriptome run
 
 ### Changed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -106,7 +106,7 @@ process {
         ]
     }
 
-    withName: ".*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN" {
+    withName: "HISAT2_ALIGN" {
         ext.args   = "--met-stderr --new-summary --dta"
         publishDir = [
             [
@@ -129,7 +129,6 @@ process {
 
             // Initialize the map with preconfigured values
             def preset_args_map = argsToMap("""
-                                            --quantMode TranscriptomeSAM
                                             --twopassMode Basic
                                             --outSAMtype BAM Unsorted
                                             --readFilesCommand zcat
@@ -275,7 +274,7 @@ process {
         ]
     }
 
-    withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION ' {
+    withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
         publishDir = [
             path: { "${params.outdir}/quality_control/rseqc/read_distribution" },
             mode: params.publish_dir_mode,

diff --git a/conf/test.config b/conf/test.config
@@ -42,7 +42,7 @@ params {
 }
 
 process {
-    withName: STAR_GENOMEGENERATE_IGENOMES {
+    withName: STAR_GENOMEGENERATE {
         ext.args = '--genomeSAindexNbases 9'
     }
 

diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -324,4 +324,4 @@
         },
         "timestamp": "2024-12-18T07:25:45.87987"
     }
-}
+}
diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
@@ -462,4 +462,4 @@
         },
         "timestamp": "2024-12-18T07:07:22.737667"
     }
-}
+}
diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "Should run with gzipped gtf": {
         "content": [
-            98
+            93
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-25T21:02:16.647189"
+        "timestamp": "2024-12-21T11:57:47.575681"
     },
     "Should run with defaults": {
         "content": [
-            97,
+            92,
             {
                 "BBMAP_PILEUP": {
                     "bbmap": 39.01,
@@ -258,9 +258,6 @@
                 "star/samtools_stats/jurkat_genome.flagstat",
                 "star/samtools_stats/jurkat_genome.idxstats",
                 "star/samtools_stats/jurkat_genome.stats",
-                "star/samtools_stats/jurkat_transcriptome.flagstat",
-                "star/samtools_stats/jurkat_transcriptome.idxstats",
-                "star/samtools_stats/jurkat_transcriptome.stats",
                 "star/star",
                 "star/star/Genome",
                 "star/star/Log.out",
@@ -353,20 +350,17 @@
                 "jurkat_genome.flagstat:md5,b5f1d127de493e406882aced667210c9",
                 "jurkat_genome.idxstats:md5,5e4a68fda75c954324d659af58d12c62",
                 "jurkat_genome.stats:md5,5bf21e33fb56e0a38b53faf34b3be2ea",
-                "jurkat_transcriptome.flagstat:md5,2e10f27f80137c7ca4d340f110aa8fcf",
-                "jurkat_transcriptome.idxstats:md5,8e38ac91c083ef3c5cf77ba782b836a5",
-                "jurkat_transcriptome.stats:md5,322d7e620bcce35529aca042d0c8b3e8",
                 "Genome:md5,612664e3cfde5e1b73ad541d93752b31",
                 "SA:md5,074ae54177bb7b9cb981382f043f36e5",
-                "SAindex:md5,1c9cd646313f1abb1cfc205ccab73464",
+                "SAindex:md5,c8cae2d81bec99f68eddc0afe570090b",
                 "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac",
                 "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee",
                 "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744",
                 "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f",
                 "exonGeTrInfo.tab:md5,ea42dd46e177f95a72a8f6a2925f7348",
                 "exonInfo.tab:md5,42a3ce2024f396b2298c0a84b07fb6e4",
                 "geneInfo.tab:md5,d0092fb1ea6fcdac270c4df788de70fb",
-                "genomeParameters.txt:md5,2fec04098057094f4b2e5a9ec4371a7d",
+                "genomeParameters.txt:md5,9e6f272d058d48c729d355ede94f8c87",
                 "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb",
                 "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9",
                 "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd",
@@ -386,7 +380,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-20T21:16:25.416797"
+        "timestamp": "2024-12-21T11:55:35.046966"
     },
     "gzip_software_versions": {
         "content": [
-Original file line number
+Diff line change
@@ Expand Up / @@ -324,4 +324,4 @@ @@
             },
             "timestamp": "2024-12-18T07:25:45.87987"
         }
-    }
+    }