NC=0 workflow error fix

RasmussenLab · Aug 7, 2023 · ba96abe · ba96abe
1 parent 311f22b
commit ba96abe
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/workflow_avamb/avamb.snake.conda.smk b/workflow_avamb/avamb.snake.conda.smk
@@ -700,7 +700,7 @@ rule write_clusters_from_nc_folders:
         "avamb"
 
     shell:
-        "sh {params.path} -d {OUTDIR}/Final_bins -o {output} ;"
+        "sh {params.path} -d {OUTDIR}/Final_bins -o {OUTDIR} ;"
         "touch {log.log_fin} "
 
 # Rename and move some files and folders 

diff --git a/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh b/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh
@@ -4,11 +4,12 @@
 while getopts "d:o:" opt; do
   case $opt in
     d) drep_dir=$OPTARG    ;;
-    o) clusters_file=$OPTARG    ;;
+    o) outdir=$OPTARG    ;;
     *) echo 'error' >&2
        exit 1
   esac
 done
+clusters_file=${outdir}/avamb/avamb_manual_drep_disjoint_clusters.tsv
 echo 'creating z y v clusters from the final set of bins'
 for s in $(ls $drep_dir)
 do