Fix workflow outputs

Signed-off-by: Ben Sherman <[email protected]>
nf-core · Dec 5, 2024 · 9e33149 · 9e33149
1 parent 26c43af
commit 9e33149
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/main.nf b/main.nf
@@ -102,14 +102,12 @@ workflow {
 
 output {
     samples {
-        path { _meta, _fastq, _md5 ->
-            { file ->
-                def dir = [
-                    'fastq': 'fastq',
-                    'md5': 'fastq/md5'
-                ][file.ext]
-                "${dir}/${file.baseName}"
-            }
+        path { _sample ->
+            def dirs = [
+                'fastq': 'fastq',
+                'md5': 'fastq/md5'
+            ]
+            return { file -> "${dirs[file.extension]}/${file.name}" }
         }
         index {
             path 'samplesheet/samplesheet.json'

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
@@ -123,14 +123,12 @@ workflow SRA {
             .map {
                 meta, fastq, md5 ->
                     def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
-                    def meta_clone = meta + [
+                    meta + [
                         fastq_1: reads[0],
                         fastq_2: reads[1] && !meta.single_end ? reads[1] : null,
                         md5_1: md5[0],
                         md5_2: md5[1] && !meta.single_end ? md5[1] : null,
                     ]
-
-                    return [ meta_clone, reads, md5 ]
             }
     }
     else {