Different matrix building

conf/hicstuff.config

@@ -130,6 +130,7 @@ params {
     hicstuff_valid_idx = 'valid_idx.pairs'
     hicstuff_min_qual = 30
     hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
+    hicstuff_bin = 10000
 }
 
 process {
@@ -165,9 +166,9 @@ process {
     }
 
     withName: 'BAM2PAIRS' {
+        ext.pairs = params.hicstuff_valid_pairs
+        ext.index = params.hicstuff_valid_idx
         ext.args = { [
-            " -o ${params.hicstuff_valid_pairs}",
-            " -x ${params.hicstuff_valid_idx}",
             " -q ${params.hicstuff_min_qual}",
             " -c ${params.hicstuff_circular}"
         ].join('').trim() }
@@ -190,6 +191,15 @@ process {
             mode: 'copy'
         ]
     }
+        withName: 'BUILD_MATRIX_COOL_ALT' {
+        ext.outname = params.hicstuff_matrix
+        ext.bin = params.hicstuff_bin
+        ext.args = {"-c1 2 -p1 3 -p2 4 -c2 5"}
+        publishDir = [
+            path: { "${params.outdir}/hicstuff/matrix" },
+            mode: 'copy'
+        ]
+    }
 
     //**********************************************
     // PREPARE_GENOME

conf/modules.config

@@ -286,4 +286,13 @@ process {
         ext.args = '--correctForMultipleTesting fdr'
         ext.prefix = { "${cool.baseName}" }
     }
+
+    withName: 'HIC_PLOT_MATRIX' {
+        publishDir = [
+            path: { "${params.outdir}/contact_maps/cool/" },
+            mode: 'copy'
+        ]
+        ext.args = '--log --perChromosome'
+        ext.prefix = { "${cool.baseName}" }
+    }
 }

modules/local/hicexplorer/hicPlotMatrix.nf

+process HIC_PLOT_MATRIX {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::hicexplorer=3.7.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
+        'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+
+
+    input:
+    tuple val(meta), path(cool)
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    hicPlotMatrix -m ${cool} -o ${prefix}_cool_log.pdf ${args}
+    """
+}

modules/local/hicstuff/bam2pairs.nf

 process BAM2PAIRS {
-    tag "$meta1"
+    tag "$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"
@@ -12,15 +12,17 @@ process BAM2PAIRS {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta1), path("valid.pairs"), emit: valid_pairs
-    tuple val(meta1), path("valid_idx.pairs"), emit: idx_pairs
+    tuple val(meta1), path("*_valid.pairs"), emit: valid_pairs
+    tuple val(meta1), path("*_valid_idx.pairs"), emit: idx_pairs
 
     script:
 
     def args = task.ext.args ?: ''
+    def pairs = task.ext.pairs ?: ''
+    def index = task.ext.index ?: ''
 
     """
-    hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} ${args}
+    hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} -o ${meta1.id}_${pairs} -x ${meta1.id}_${index} ${args}
     """
 
 }

modules/local/hicstuff/build_matrix_cool_alt.nf

+process BUILD_MATRIX_COOL_ALT {
+    tag "$meta1.id"
+    label 'process_single'
+
+    conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
+    container = "lbmc/hicstuff:3.1.3"
+
+    input:
+    tuple val(meta), path(chromosome_size)
+    tuple val(meta1), path(idx_pairs)
+
+
+    output:
+    tuple val(meta), path("${meta1.id}_*.cool"), emit: matrix
+
+    script:
+
+    def args = task.ext.args ?: ''
+    def bin = task.ext.bin.toInteger() ?: ''
+    def outname = task.ext.outname ?: ''
+    def base = outname.replaceFirst(/.txt/,"")
+
+    """
+    cooler cload pairs ${args} ${chromosome_size}:${bin} ${idx_pairs} ${base}.cool
+
+    mv ${base}.cool ${meta1.id}_${base}_${bin}_alt.cool
+    """
+}

subworkflows/local/hicstuff_sub.nf

@@ -4,6 +4,7 @@ include { FRAGMENT_ENZYME } from '../../modules/local/hicstuff/fragment_enzyme'
 include { BAM2PAIRS } from '../../modules/local/hicstuff/bam2pairs'
 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'
 
 // Paired-end to Single-end
 def pairToSingle(row, mates) {
@@ -33,6 +34,7 @@ workflow HICSTUFF_SUB {
     ligation_site
     digestion
     fasta
+    chromosome_size
 
     main:
 
@@ -55,20 +57,29 @@ workflow HICSTUFF_SUB {
         BOWTIE2_ALIGNMENT.out.bam.combine(BOWTIE2_ALIGNMENT.out.bam)
             .map {
                 meta1, bam1, meta2, bam2 ->
-                    meta1.id == meta2.id && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
+                    meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
         },
         FRAGMENT_ENZYME.out.info_contigs.collect(),
         digestion,
         fasta.collect()
     )
 
+
+    //TODO rajouter filtres + distance law + filtres PCR en options
+    // pour les PCR filter, soit le hicstuff soit PICARD
+
     BUILD_MATRIX(
         BAM2PAIRS.out.idx_pairs,
-        FRAGMENT_ENZYME.out.fragments_list
+        FRAGMENT_ENZYME.out.fragments_list.collect()
     )
 
     BUILD_MATRIX_COOL(
         BAM2PAIRS.out.idx_pairs,
-        FRAGMENT_ENZYME.out.fragments_list
+        FRAGMENT_ENZYME.out.fragments_list.collect()
+    )
+
+    BUILD_MATRIX_COOL_ALT(
+        chromosome_size.collect(),
+        BAM2PAIRS.out.idx_pairs
     )
 }

workflows/hicstuff.nf

@@ -39,6 +39,7 @@ workflow HICSTUFF {
         PREPARE_GENOME.out.index,
         ch_ligation_site,
         params.digestion, //str enzyme
-        ch_fasta
+        ch_fasta,
+        PREPARE_GENOME.out.chromosome_size
     )
 }