Merge pull request #197 from maxibor/dev

Fix of #189

Author: apeltzer

bin/extract_map_reads.py

@@ -19,10 +19,10 @@ def _get_args():
     parser.add_argument('bam_file', help="path to bam file")
     parser.add_argument('fwd', help='path to forward fastq file')
     parser.add_argument(
-        '-2',
+        '-rev',
         dest="rev",
         default=None,
-        help="path to forward fastq file")
+        help="path to reverse fastq file")
     parser.add_argument(
         '-of',
         dest="out_fwd",
@@ -163,8 +163,8 @@ def write_fq(fq_dict, fname, mode):
     """
     Write to fastq file
     INPUT:
-    - fq_dict(dict) dictionary with unmapped read names as keys, seq and quality as values
-        in a list
+    - fq_dict(dict) dictionary with unmapped read names as keys, 
+        unmapped/mapped (u|m), seq, and quality as values in a list
     - fname(string) Path to output fastq file
     - mode(string) strip (remove read) or replace (replace read sequence) by Ns
     """
@@ -218,6 +218,11 @@ def write_fq(fq_dict, fname, mode):
                             f.write(f"{i}\n")
 
 
+def check_strip_mode(mode):
+    if mode.lower() not in ['replace', 'strip']:
+        print(f"Mode must be {' or '.join(mode)}")
+
+
 if __name__ == "__main__":
     BAM, IN_FWD, IN_REV, OUT_FWD, OUT_REV, MODE, PROC = _get_args()
 

main.nf

@@ -947,14 +947,14 @@ process strip_input_fastq {
         out_fwd = bam.baseName+'.stripped.fq.gz'
         """
         samtools index $bam
-        extract_map_reads.py $bam ${fq[0]} -of $out_fwd -p ${task.cpus}
+        extract_map_reads.py $bam ${fq[0]} -m ${params.strip_mode} -of $out_fwd -p ${task.cpus}
         """
     } else {
         out_fwd = bam.baseName+'.stripped.fwd.fq.gz'
         out_rev = bam.baseName+'.stripped.rev.fq.gz'
         """
         samtools index $bam
-        extract_map_reads.py $bam ${fq[0]} -2 ${fq[0]} -of $out_fwd -or $out_rev -p ${task.cpus}
+        extract_map_reads.py $bam ${fq[0]} -rev ${fq[1]} -m  ${params.strip_mode} -of $out_fwd -or $out_rev -p ${task.cpus}
         """ 
     }