ARGS hicstuff bam2pairs

conf/hicstuff.config

@@ -126,6 +126,9 @@ params {
     hicstuff_output_frags = 'fragments_list.txt'
     hicstuff_frags_plot = 'False'
     hicstuff_frags_plot_path = 'frags_hist.pdf'
+    hicstuff_valid_pairs = 'valid.pairs'
+    hicstuff_valid_idx = 'valid_idx.pairs'
+    hicstuff_min_qual = 30
 }
 
 process {
@@ -161,6 +164,11 @@ process {
     }
 
     withName: 'BAM2PAIRS' {
+        ext.args = { [
+            " -o ${params.hicstuff_valid_pairs}",
+            " -x ${params.hicstuff_valid_idx}",
+            " -q ${params.hicstuff_min_qual}"
+        ].join('').trim() }
         publishDir = [
             path: { "${params.outdir}/hicstuff/pairs" },
             mode: 'copy'

modules/local/hicstuff/bam2pairs.nf

@@ -16,8 +16,11 @@ process BAM2PAIRS {
     tuple val(meta1), path("valid_idx.pairs"), emit: idx_pairs
 
     script:
+
+    def args = task.ext.args ?: ''
+
     """
-    hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -o valid.pairs -x valid_idx.pairs -i ${info_contigs} -q 30 -e ${digestion} -f ${fasta}
+    hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} ${args}
     """
 
 }