Use zcat -f for fastqs to allow compressed and/or uncompressed files

aryeelab · Jan 29, 2019 · cf37fb8 · cf37fb8
1 parent 3ff836c
commit cf37fb8
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/preprocess_hic.wdl b/preprocess_hic.wdl
@@ -74,8 +74,8 @@ task split_fastq_files {
     Int disk_gb
 
     command {
-        zcat ${sep=' ' r1_in} | split -d --suffix-length=3 -l ${num_lines_per_chunk} --additional-suffix='_R1.fastq' --filter='gzip > $FILE.gz' - ${sample_id}-
-        zcat ${sep=' ' r2_in} | split -d --suffix-length=3 -l ${num_lines_per_chunk} --additional-suffix='_R2.fastq' --filter='gzip > $FILE.gz' - ${sample_id}-
+        zcat -f ${sep=' ' r1_in} | split -d --suffix-length=3 -l ${num_lines_per_chunk} --additional-suffix='_R1.fastq' --filter='gzip > $FILE.gz' - ${sample_id}-
+        zcat -f ${sep=' ' r2_in} | split -d --suffix-length=3 -l ${num_lines_per_chunk} --additional-suffix='_R2.fastq' --filter='gzip > $FILE.gz' - ${sample_id}-
     }
 
      runtime {
@@ -125,7 +125,7 @@ task count_pairs {
     String dollar = "$"
 
     command <<<
-        num_lines=`zcat ${sep=' ' r1_fastq} | wc -l`
+        num_lines=`zcat -f ${sep=' ' r1_fastq} | wc -l`
         let "num_pairs=${dollar}num_lines/4"
         echo ${dollar}num_pairs
     >>>