reverted to version 39.01

UPHL-BioNGS · Apr 24, 2024 · 0252e5b · 0252e5b
1 parent 031e2fd
commit 0252e5b
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/modules/local/bbduk.nf b/modules/local/bbduk.nf
@@ -2,8 +2,8 @@ process bbduk {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/bbtools:39.06'
-  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  container     'staphb/bbtools:39.01'
+  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -32,7 +32,7 @@ process bbduk {
       out1=bbduk/${prefix}_rmphix_R1.fastq.gz \
       out2=bbduk/${prefix}_rmphix_R2.fastq.gz \
       outm=bbduk/${prefix}.matched_phix.fastq.gz \
-      ref=/bbmap/resources/phix174_ill.ref.fa.gz \
+      ref=/opt/bbmap/resources/phix174_ill.ref.fa.gz \
       stats=bbduk/${prefix}.phix.stats.txt \
       threads=${task.cpus} \
       | tee -a \$log_file
@@ -43,3 +43,5 @@ process bbduk {
     END_VERSIONS
   """
 }
+
+//ref=/bbmap/resources/phix174_ill.ref.fa.gz \