fix module for downloading PACBIO data

modules/get_fastq.nf

@@ -15,7 +15,6 @@ process GET_FASTQ {
   def sra_ids = "${sra_ids.replaceAll(~/\s/,'')}"
   """
   fasterq-dump \\
-    --include-technical \\
     --split-files \\
     --threads $task.cpus \\
     --outdir ./${sra_ids}_data \\
@@ -26,12 +25,25 @@ process GET_FASTQ {
   if [ \$(grep -ic "is PACBIO, please use fastq-dump instead" fasterq-dump.err) -eq 1 ]
   then
       fastq-dump \\
-        --split-files \\
+        --gzip \\
         --outdir ./${sra_ids}_data \\
         $sra_ids
   else
     echo "fasterq-dump error was:"
     cat fasterq-dump.err
   fi
+
+  # make sure they have right extension
+  for i in \$( find ./${sra_ids}_data -name "*.fq" ) ; do
+    mv \$i \${i%%.fq}.fastq ;
+  done
+  for i in \$( find ./${sra_ids}_data -name "*.fq.gz" ) ; do
+    mv \$i \${i%%.fq.gz}.fastq.gz ;
+  done
+
+  # make sure data is compressed
+  for i in \$( find ./${sra_ids}_data -name "*.fastq" ) ; do
+    gzip \$i ;
+  done
   """
 }