Added a fastq_merge.sh to replace the python version

bin/merge_fastq.py

@@ -38,7 +38,7 @@
     if (re.match(r"^.*(_2.fastq)$", fastq_filename) and handles['_2.fastq'] is None):
         handles['_2.fastq'] = open(args.out_prefix + '_2.fastq', "w")
 
-# Now open each file and merge the records into the appropirate
+# Now open each file and merge the records into the appropriate
 # output file.
 for fastq_filename in args.fastq_files:
     fh = None

bin/merge_fastq.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+sample_id=$1
+
+files_1=(`find . -maxdepth 1 -name "*_1.fastq" | grep -v $sample_id | sort`)
+files_2=(`find . -maxdepth 1 -name "*_2.fastq" | grep -v $sample_id | sort`)
+
+# Check the number of files. If there is more than one then
+# combine them. If not, then just create a link with the
+# sample_id as the name.
+if [ ${#files_1[@]} -gt 1 ] ; then
+
+    for i in "${!files_1[@]}"; do
+        cat ${files_1[$i]} >> ${sample_id}_1.fastq
+    done;
+
+elif [ ${#files_1[@]} -eq 1 ] ; then
+
+    ln ${files_1[0]} ${sample_id}_1.fastq
+
+fi
+
+# If there are paired files.
+if [ ${#files_2[@]} -gt 1 ] ; then
+
+    for i in "${!files_2[@]}"; do
+        cat ${files_2[$i]} >> ${sample_id}_2.fastq
+    done;
+
+elif [ ${#files_2[@]} -eq 1 ] ; then
+
+    ln ${files_2[0]} ${sample_id}_2.fastq
+fi
+

modules/local/fastq_merge.nf

@@ -3,7 +3,6 @@
  */
 process fastq_merge {
     tag { sample_id }
-    container "systemsgenetics/gemmaker:2.1.0"
 
     input:
     tuple val(sample_id), path(fastq_files)
@@ -14,6 +13,6 @@ process fastq_merge {
 
     script:
     """
-    merge_fastq.py --fastq_files ${fastq_files.join(" ")} --out_prefix ${sample_id}
+    merge_fastq.sh ${sample_id}
     """
 }