get absolute path for outdir

CDCgov · May 31, 2024 · 7d8c956 · 7d8c956
1 parent 739d98f
commit 7d8c956
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/modules/local/summarize_qc.nf b/modules/local/summarize_qc.nf
@@ -15,12 +15,14 @@ process SUMMARIZE_QC {
 
     script: // This script is bundled with the pipeline, in polkapox/bin/
     def args = task.ext.args   ?: ''
-    """
+    // Convert relative path to absolute path
+    def absolute_outdir = file(params.outdir)
+
     summarize_qc.py \\
         --analysis_dir . \\
         --samplesheet $samplesheet \\
         --reference_genome ${params.fasta} \\
-        --project_outdir ${params.outdir} \\
+        --project_outdir ${absolute_outdir} \\
         --kraken_db ${params.kraken_db} \\
         --kraken_tax_ids ${params.kraken2_tax_ids} \\
         --filter ${params.filter} \\