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Verified Commit 104f1db4 authored by Mia Croiset's avatar Mia Croiset
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delete build_matrix_cool_alt which is useless now

parent c85adfeb
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......@@ -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: { "${params.outdir}/hicstuff/matrix" },
mode: 'copy'
]
}
//*****************************************
// QUALITY METRICS
......
process BUILD_MATRIX_COOL_ALT {
tag "$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
"""
}
......@@ -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
}
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