Change output of mapped_3hic_fragments.py

CHANGELOG.md

 # nf-core/hic: Changelog
 
-
 ## v1.1dev
 
+* Add --saveInteractionBAM option
 * Fix bug for reads extension _1/_2 (#30)
-
 * Update manual (#28)
 
 ## v1.0 - 2019-05-06

bin/mapped_2hic_fragments.py

@@ -53,7 +53,7 @@ def get_args():
              "minInsertSize=", "maxInsertSize", 
              "minFragSize", "maxFragSize", 
              "minDist",
-             "gatg", "samOut", "verbose", "all", "help"])
+             "gatg", "sam", "verbose", "all", "help"])
     except getopt.GetoptError:
         usage()
         sys.exit(-1)
@@ -442,7 +442,7 @@ def get_interaction_type(read1, read1_chrom, resfrag1, read2,
     # If returned InteractionType=None -> Same restriction fragment
     # and same strand = Dump
     interactionType = None
- 
+      
     if not read1.is_unmapped and not read2.is_unmapped and resfrag1 is not None and resfrag2 is not None:
         # same restriction fragment
         if resfrag1 == resfrag2:
@@ -501,9 +501,9 @@ if __name__ == "__main__":
             minInsertSize = arg
         elif opt in ("-l", "--longestInsertSize"):
             maxInsertSize = arg
-        elif opt in ("-t", "--shortestFragmentSize"):
+        elif opt in ("-t", "--shortestFragmentLength"):
             minFragSize = arg
-        elif opt in ("-m", "--longestFragmentSize"):
+        elif opt in ("-m", "--longestFragmentLength"):
             maxFragSize = arg
         elif opt in ("-d", "--minCisDist"):
             minDist = arg
@@ -613,6 +613,7 @@ if __name__ == "__main__":
                 r2_chrom = None
 
             if r1_resfrag is not None or r2_resfrag is not None:
+
                 interactionType = get_interaction_type(r1, r1_chrom, r1_resfrag, r2, r2_chrom, r2_resfrag, verbose)
                 dist = get_PE_fragment_size(r1, r2, r1_resfrag, r2_resfrag, interactionType)
                 cdist = get_cis_dist(r1, r2)
@@ -724,10 +725,14 @@ if __name__ == "__main__":
 
                     if or1_resfrag is not None:
                         or1_fragname = or1_resfrag.value['name']
-                    
+                    else:
+                        or1_fragname = 'None'
+                        
                     if or2_resfrag is not None:
                         or2_fragname = or2_resfrag.value['name']
-                    
+                    else:
+                        or2_fragname = 'None'
+                        
                     cur_handler.write(
                         or1.qname + "\t" +
                         or1_chrom + "\t" +

conf/hicpro.config

@@ -38,5 +38,6 @@ params {
 
        saveReference = false
        saveAlignedIntermediates = false
+       saveInteractionBAM = false
 }
 

main.nf

@@ -32,6 +32,8 @@ def helpMessage() {
       --fasta                            Path to Fasta reference
       --chromosome_size                  Path to chromosome size file
       --restriction_fragments            Path to restriction fragment file (bed)
+      --saveReference                    Save reference genome to output folder. Default: False
+      --saveAlignedIntermediates         Save intermediates alignment files. Default: False
 
     Options:
       --bwt2_opts_end2end                Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
@@ -43,8 +45,9 @@ def helpMessage() {
       --max_restriction_framgnet_size    Maximum size of restriction fragmants to consider. Default: None
       --min_insert_size                  Minimum insert size of mapped reads to consider. Default: None
       --max_insert_size                  Maximum insert size of mapped reads to consider. Default: None
+      --saveInteractionBAM               Save BAM file with interaction tags (dangling-end, self-circle, etc.). Default: False
 
-      --dnase                            Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: false
+      --dnase                            Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: False
 
       --min_cis_dist                     Minimum intra-chromosomal distance to consider. Default: None
       --rm_singleton                     Remove singleton reads. Default: true
@@ -65,10 +68,10 @@ def helpMessage() {
 
     Step options:
 
-      --skip_maps                        Skip generation of contact maps. Useful for capture-C. Default: false
-      --skip_ice                         Skip ICE normalization. Default: false
-      --skip_cool                        Skip generation of cool files. Default: false
-      --skip_multiQC                     Skip MultiQC. Default: false
+      --skip_maps                        Skip generation of contact maps. Useful for capture-C. Default: False
+      --skip_ice                         Skip ICE normalization. Default: False
+      --skip_cool                        Skip generation of cool files. Default: False
+      --skip_multiQC                     Skip MultiQC. Default: False
 
     AWSBatch options:
       --awsqueue                         The AWSBatch JobQueue that needs to be set when running on AWSBatch
@@ -154,7 +157,7 @@ if ( params.splitFastq ){
    raw_reads_full = raw_reads.concat( raw_reads_2 )
    raw_reads = raw_reads_full.splitFastq( by: params.splitFastq , file: true)
  }else{
-   raw_reads = raw_reads.concat( raw_reads_2 )
+   raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag: "data")
 }
 
 
@@ -599,6 +602,10 @@ if (!params.dnase){
       output:
          set val(sample), file("*.validPairs") into valid_pairs
          set val(sample), file("*.validPairs") into valid_pairs_4cool
+	 set val(sample), file("*.DEPairs") into de_pairs
+	 set val(sample), file("*.SCPairs") into sc_pairs
+         set val(sample), file("*.REPairs") into re_pairs
+	 set val(sample), file("*.FiltPairs") into filt_pairs
          set val(sample), file("*RSstat") into all_rsstat
 
       script:
@@ -612,9 +619,10 @@ if (!params.dnase){
          if ("$params.max_insert_size".isInteger()) opts="${opts} -l ${params.max_insert_size}"
          if ("$params.min_restriction_fragment_size".isInteger()) opts="${opts} -t ${params.min_restriction_fragment_size}"
          if ("$params.max_restriction_fragment_size".isInteger()) opts="${opts} -m ${params.max_restriction_fragment_size}"
+	 if (params.saveInteractionBAM) opts="${opts} --sam"
 
          """
-         mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} ${opts}
+         mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
          """
    }
 }