Fixed bug --config

mazzalab · Sep 26, 2023 · bca4aab · bca4aab
1 parent 19afaac
commit bca4aab
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/pipeline/fix_wipe_pairs_reads_parallel.smk b/pipeline/fix_wipe_pairs_reads_parallel.smk
@@ -1,4 +1,4 @@
-#cmd: snakemake --config sample_name=sample --config chunk_size=50000000 -s pipeline/fix_wipe_pairs_reads_parallel.smk --use-conda --cores 4
+#cmd: snakemake --config sample_name=sample chunk_size=50000000 -s pipeline/fix_wipe_pairs_reads_parallel.smk --use-conda --cores 4
 
 import os
 import shutil

diff --git a/pipeline/fix_wipe_single_reads_parallel.smk b/pipeline/fix_wipe_single_reads_parallel.smk
@@ -1,4 +1,4 @@
-#cmd: snakemake --config sample_name=sample_R1 --config chunk_size=50000000 -s pipeline/fix_wipe_single_reads_parallel.smk --use-conda --cores 4
+#cmd: snakemake --config sample_name=sample_R1 chunk_size=50000000 -s pipeline/fix_wipe_single_reads_parallel.smk --use-conda --cores 4
 
 import os
 import shutil

diff --git a/run_wiping.sh b/run_wiping.sh
@@ -10,7 +10,7 @@ then
   if [ $cores > 1 ]
   then
     echo "Processing paired-end files in parallel"
-    snakemake --config sample_name=$sample_name --config chunk_size=$chunk_size -s pipeline/fix_wipe_pairs_reads_parallel.smk --use-conda --cores $cores
+    snakemake --config sample_name=$sample_name chunk_size=$chunk_size -s pipeline/fix_wipe_pairs_reads_parallel.smk --use-conda --cores $cores
   else
     echo "Processing paired-end files sequentially"
     snakemake --config sample_name=$sample_name -s pipeline/fix_wipe_pairs_reads_sequential.smk --use-conda --cores $cores
@@ -19,7 +19,7 @@ else
   if [ $cores > 1 ]
   then
     echo "Processing single-end file in parallel"
-    snakemake --config sample_name=$sample_name --config chunk_size=$chunk_size -s pipeline/fix_wipe_single_reads_parallel.smk --use-conda --cores $cores
+    snakemake --config sample_name=$sample_name chunk_size=$chunk_size -s pipeline/fix_wipe_single_reads_parallel.smk --use-conda --cores $cores
   else
     echo "Processing single-end file sequentially"
     snakemake --config sample_name=$sample_name -s pipeline/fix_wipe_single_reads_sequential.smk --use-conda --cores $cores