rewrite so it works

tasks/utilities/file_handling/task_cat_lanes.wdl

@@ -25,38 +25,23 @@ task cat_lanes {
   command <<<
     # exit task if anything throws an error (important for proper gzip format)
     set -euo pipefail
+
+    exists() { [[ -f $1 ]]; }
 
-    # move reads into single directory
-    mkdir -v reads
-    mv -v ~{read1_lane1} \
-          ~{read2_lane1} \
-          ~{read1_lane2} \
-          ~{read2_lane2} \
-          ~{read1_lane3} \
-          ~{read2_lane3} \
-          ~{read1_lane4} \
-          ~{read2_lane4} \
-      reads/
+    set -euo pipefail
 
-    # check for valid gzipped format (this task assumes FASTQ files are gzipped - they should be coming from ILMN instruments)
-    gzip -t reads/*.gz
+    cat ~{read1_lane1} ~{read1_lane2} ~{read1_lane3} ~{read1_lane4} > "~{samplename}_merged_R1.fastq.gz"
 
-    # run concatenate script and send STDOUT/ERR to STDOUT
-    # reminder: script will skip over samples that only have R1 file present
-    # reminder: script REQUIRES standard illumina file endings like: _L001_R1_001.fastq.gz and _L002_R2_001.fastq.gz
-    # see script here: https://github.com/theiagen/utilities/blob/main/scripts/concatenate-across-lanes.sh
-    concatenate-across-lanes.sh reads/
+    if exists ~{read2_lane1} ; then
+      cat ~{read2_lane1} ~{read2_lane2} ~{read2_lane3} ~{read2_lane4} > "~{samplename}_merged_R2.fastq.gz"
+    fi
 
     # ensure newly merged FASTQs are valid gzipped format
-    gzip -t reads/*merged*.gz
-
-    # determine output filenames for outputs
-    mv -v reads/*_merged_R1.fastq.gz reads/~{samplename}_merged_R1.fastq.gz
-    mv -v reads/*_merged_R2.fastq.gz reads/~{samplename}_merged_R2.fastq.gz
+    gzip -t *merged*.gz
   >>>
   output {
-    File read1_concatenated = "reads/~{samplename}_merged_R1.fastq.gz"
-    File? read2_concatenated = "reads/~{samplename}_merged_R2.fastq.gz"
+    File read1_concatenated = "~{samplename}_merged_R1.fastq.gz"
+    File? read2_concatenated = "~{samplename}_merged_R2.fastq.gz"
   }
   runtime {
     docker: "~{docker}"