Merge pull request #194 from danilodileo/fix-small-issues

Fix small issues
nf-core · Oct 17, 2023 · 90887dc · 90887dc
2 parents de8f83b + 19f74da
commit 90887dc
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -401,7 +401,11 @@ process {
         publishDir = [
             path: "${params.outdir}/multiqc",
             mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            path: "${params.outdir}/summary_tables",
+            mode: 'copy',
+            pattern: '*.html',
+            saveAs: { filename -> "${params.assembler}.${params.orf_caller}.multiqc_report.html" }
         ]
     }
 }
diff --git a/nextflow.config b/nextflow.config
@@ -69,7 +69,7 @@ params {
     save_cat_db                 = false
 
     // Eukulele options
-    eukulele_db                 = null
+    eukulele_db                 = ''
     dbname                      = null
     skip_eukulele               = false
     eukulele_dbpath             = './eukulele/'

diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf
@@ -337,7 +337,7 @@ workflow METATDENOVO {
             .map { [ [ id: 'megahit' ], it ] }
             .set { ch_assembly_contigs }
         ch_versions = ch_versions.mix(MEGAHIT_INTERLEAVED.out.versions)
-    }
+    } else { exit 1, 'Assembler not specified!' }
 
     // If the user asked for length filtering, perform that with SEQTK_SEQ (the actual length parameter is used in modules.config)
     if ( params.min_contig_length > 0 ) {