delete build_matrix_cool_alt which is useless now

conf/modules.config

@@ -274,15 +274,6 @@ 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'
-        ]
-    }
 
     //*****************************************
     // QUALITY METRICS

modules/local/hicstuff/build_matrix_cool_alt.nf

-process BUILD_MATRIX_COOL_ALT {
-    tag "$meta1.id"
-    label 'process_single'
-
-    conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
-    container = "docker.io/lbmc/hicstuff:3.1.3"
-
-    input:
-    tuple val(meta), path(chromosome_size)
-    tuple val(meta1), path(idx_pairs)
-
-
-    output:
-    tuple val(meta), path("${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.nf

@@ -4,7 +4,6 @@ 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'
 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'
@@ -50,19 +49,6 @@ workflow HICSTUFF {
     ch_reads_r2 = reads.map{ it -> pairToSingle(it,"R2") }
     ch_reads = ch_reads_r1.concat(ch_reads_r2)
 
-/*     if (params.cutsite){
-        ch_reads.combine(ch_reads)
-        .map {
-            meta1, reads1, meta2, reads2 ->
-                meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
-        }.set{ new_ch_reads }
-        CUTSITE(
-            new_ch_reads,
-            digestion
-        )
-        ch_reads = CUTSITE.out.fastq
-    } */
-
     if (params.iteralign && params.cutsite) {
         error "Error: iteralign and cutsite can't both be true at the same time! Set one of them false"
     }
@@ -160,13 +146,7 @@ workflow HICSTUFF {
         FRAGMENT_ENZYME.out.fragments_list.collect()
     )
 
-   /*  BUILD_MATRIX_COOL_ALT(
-        chromosome_size.collect(),
-        ch_idx_pairs
-    ) */
-
     emit:
-    //cool = BUILD_MATRIX_COOL_ALT.out.matrix
     pairs = ch_pairs
     versions = ch_versions
 }