fix: correct file name for combined kraken2 reports

nf-core · Apr 6, 2024 · 46e6637 · 46e6637
1 parent 2c430aa
commit 46e6637
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Showing 2 changed files with 7 additions and 15 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -502,7 +502,7 @@ process {
     }
 
     withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
-        ext.prefix = { "kraken2_${meta.db_name}_combined_reports" }
+        ext.prefix = { "kraken2_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/kraken2/" },
             mode: params.publish_dir_mode,

diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
@@ -170,22 +170,14 @@ workflow STANDARDISATION_PROFILES {
     // Have to sort by size to ensure first file actually has hits otherwise
     // the script fails
     ch_profiles_for_kraken2 = groupProfiles(
-        ch_input_profiles.kraken2.map { meta, profile ->
-            def new_meta = [
-                // Replace the tool name to get the right output-format description.
-                tool: meta.tool == 'kraken2-bracken' ? 'kraken2' : meta.tool,
-                // Append so as to disambiguate when we have same databases
-                // for kraken2 step of bracken, with normal bracken.
-                id: meta.tool,
-                // Append so as to disambiguate when we have same databases
-                // for kraken2 step of bracken, with normal bracken.
-                db_name: meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}"
-
-            ]
-            return [meta + new_meta, profile]
+        ch_input_profiles.kraken2.dump(tag: 'k2-profiles', pretty: true)
+        .map { meta, profile ->
+            // Replace database name, to get the right output description.
+            def db_name = meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}"
+            return [meta + [db_name: db_name], profile]
         },
         [sort: { -it.size() }]
-    )
+    ).dump(tag: 'k2-grouped', pretty: true)
 
     KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 )
     ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )