hicstuff distance law option

conf/hicstuff.config

@@ -121,7 +121,7 @@ params {
     // Hicstuff
     hicstuff_bwt2_align_opts = '--very-sensitive-local'
     hicstuff_min_size = 0
-    hicstuff_circular = 'frue'
+    hicstuff_circular = 'false'
     hicstuff_output_contigs = 'info_contigs.txt'
     hicstuff_output_frags = 'fragments_list.txt'
     hicstuff_frags_plot = 'false'
@@ -135,9 +135,18 @@ params {
     hicstuff_plot_events = 'false'
     hicstuff_pie_plot = 'distrib'
     hicstuff_dist_plot = 'dist'
+    hicstuff_centro_file = 'None'       //give absolute path or 'None'
+    hicstuff_base = 1.1
+    hicstuff_distance_out_file = 'distance_law.txt'
+    hicstuff_rm_centro = 'None'         //int or 'None'
+    hicstuff_distance_plot = 'false'
+    hicstuff_distance_out_plot = 'plot_distance_law.pdf'
 
     //Hicstuff optional modules
     filter_event = true
+    distance_law = true
+    filter_pcr = true
+    filter_pcr_picard = false
 }
 
 process {
@@ -198,6 +207,22 @@ process {
         ]
     }
 
+    withName: 'DISTANCE_LAW' {
+        ext.args = { [
+            " -c ${params.hicstuff_centro_file}",
+            " -b ${params.hicstuff_base}",
+            " -o ${params.hicstuff_distance_out_file}",
+            " -u ${params.hicstuff_circular}",
+            " -r ${params.hicstuff_rm_centro}",
+            " -l ${params.hicstuff_distance_plot}",
+            " -d ${params.hicstuff_distance_out_plot}"
+        ].join('').trim() }
+        publishDir = [
+            path: { "${params.outdir}/hicstuff/pairs" },
+            mode: 'copy'
+        ]
+    }
+
     withName: 'BUILD_MATRIX' {
         ext.args = params.hicstuff_matrix
         publishDir = [

modules/local/hicstuff/distance_law.nf

+process DISTANCE_LAW {
+    tag "$meta1.id"
+    label 'process_high'
+
+    conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
+    container = "lbmc/hicstuff:3.1.3"
+
+    input:
+    tuple val(meta1), path(idx_pairs)
+    tuple val(meta), path(fragments_list)
+
+    output:
+    path("*distance_law.txt")
+    path("*.pdf"), optional: true
+
+    script:
+
+    def args = task.ext.args ?: ''
+
+    """
+    hicstuff_distance_law.py -i ${idx_pairs} -f ${fragments_list} -p ${meta1.id} ${args}
+    """
+}

subworkflows/local/hicstuff_sub.nf

@@ -6,6 +6,8 @@ include { BUILD_MATRIX } from '../../modules/local/hicstuff/build_matrix'
 include { BUILD_MATRIX_COOL } from '../../modules/local/hicstuff/build_matrix_cool'
 include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matrix_cool_alt'
 include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
+include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
+include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
 
 // Paired-end to Single-end
 def pairToSingle(row, mates) {
@@ -73,6 +75,15 @@ workflow HICSTUFF_SUB {
         FILTER_EVENT.out.idx_pairs_filtered.set{ ch_idx_pairs }
     }
 
+    if ( params.distance_law ){
+        DISTANCE_LAW(
+            ch_idx_pairs,
+            FRAGMENT_ENZYME.out.fragments_list.collect()
+        )
+    }
+
+
+
     //TODO rajouter filtres + distance law + filtres PCR en options
     // pour les PCR filter, soit le hicstuff soit PICARD