refactorisation remove gatk module

modules/nf-core/custom/gatk4/markduplicates/main.nf

-process GATK4_MARKDUPLICATES {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::gatk4=4.4.0.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(bam)
-    path  fasta
-    path  fasta_fai
-
-    output:
-    tuple val(meta), path("*cram"),     emit: cram,  optional: true
-    tuple val(meta), path("*bam"),      emit: bam,   optional: true
-    tuple val(meta), path("*.crai"),    emit: crai,  optional: true
-    tuple val(meta), path("*.bai"),     emit: bai,   optional: true
-    tuple val(meta), path("*.metrics"), emit: metrics
-    path "versions.yml",                emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
-    def input_list = bam.collect{"--INPUT $it"}.join(' ')
-    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
-
-    def avail_mem = 3072
-    if (!task.memory) {
-        log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
-    }
-    """
-    gatk --java-options "-Xmx${avail_mem}M" MarkDuplicates \\
-        $input_list \\
-        --OUTPUT ${prefix} \\
-        --METRICS_FILE ${prefix}.metrics \\
-        --TMP_DIR . \\
-        ${reference} \\
-        $args
-    if  [[ ${prefix} == *.cram ]]&&[[ -f ${prefix}.bai ]]; then
-        mv ${prefix}.bai ${prefix}.crai
-    fi
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
-    END_VERSIONS
-    """
-}
\ No newline at end of file

modules/nf-core/custom/gatk4/markduplicates/meta.yml

-name: gatk4_markduplicates
-description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
-keywords:
-  - markduplicates
-  - bam
-  - sort
-tools:
-  - gatk4:
-      description:
-        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
-        with a primary focus on variant discovery and genotyping. Its powerful processing engine
-        and high-performance computing features make it capable of taking on projects of any size.
-      homepage: https://gatk.broadinstitute.org/hc/en-us
-      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
-      tool_dev_url: https://github.com/broadinstitute/gatk
-      doi: 10.1158/1538-7445.AM2017-3590
-      licence: ["MIT"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: Sorted BAM file
-      pattern: "*.{bam}"
-  - fasta:
-      type: file
-      description: Fasta file
-      pattern: "*.{fasta}"
-  - fasta_fai:
-      type: file
-      description: Fasta index file
-      pattern: "*.{fai}"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - bam:
-      type: file
-      description: Marked duplicates BAM file
-      pattern: "*.{bam}"
-  - cram:
-      type: file
-      description: Marked duplicates CRAM file
-      pattern: "*.{cram}"
-  - bai:
-      type: file
-      description: BAM index file
-      pattern: "*.{bam.bai}"
-  - crai:
-      type: file
-      description: CRAM index file
-      pattern: "*.{cram.crai}"
-  - metrics:
-      type: file
-      description: Duplicate metrics file generated by GATK
-      pattern: "*.{metrics.txt}"
-
-authors:
-  - "@ajodeh-juma"
-  - "@FriederikeHanssen"
-  - "@maxulysse"
\ No newline at end of file

subworkflows/local/hicstuff_sub.nf

@@ -8,7 +8,6 @@ include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matri
 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'
-include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
 include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
 include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
 include { FILTER_PAIR } from '../../modules/local/filterbam/main'
@@ -137,9 +136,6 @@ workflow HICSTUFF_SUB {
         FILTER_PCR.out.idx_pairs_pcrfree.set{ ch_idx_pairs }
     }
 
-    //TODO rajouter filtres + distance law + filtres PCR en options
-    // pour les PCR filter, soit le hicstuff soit PICARD
-
     BUILD_MATRIX(
         ch_idx_pairs,
         FRAGMENT_ENZYME.out.fragments_list.collect()