Hicexplorer hicpca

modules/nf-core/hicexplorer/hicpca/main.nf

@@ -0,0 +1,56 @@
+process HICEXPLORER_HICPCA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::hicexplorer=3.7.2 numpy=1.23.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1':
+        'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(matrix)
+
+    output:
+    tuple val(meta), path("${prefix}_*")           , emit:results
+    tuple val(meta), path("${prefix}_pca1.$format"), emit:pca1
+    tuple val(meta), path("${prefix}_pca2.$format"), emit:pca2
+    path("versions.yml")                           , emit:versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    args     = args.tokenize()
+    def idx  = args.findIndexOf{ it == '--format' | it == '-f' }
+    format   = 'bigwig'
+    if (idx>=0) {
+        format = args[idx+1]
+        args.remove(idx+1)
+        args.remove(idx)
+    }
+    idx = args.indexOf('--whichEigenvectors')
+    eigenvectors = '1 2'
+    if(idx>=0) {
+        eigenvectors = args[idx + 1]
+        args.remove(idx+1)
+        args.remove(idx)
+    }
+    outfilenames = eigenvectors.tokenize()
+        .collect{"${prefix}_pca${it}.${format}"}.join(' ')
+    args = args.join(' ')
+    """
+    hicPCA \\
+        -m $matrix \\
+        $args \\
+        --format $format \\
+        --whichEigenvectors $eigenvectors \\
+        --outputFileName $outfilenames
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hicexplorer: \$(hicPCA --version 2>&1 | sed 's/hicPCA //')
+    END_VERSIONS
+    """
+}

modules/nf-core/hicexplorer/hicpca/meta.yml

@@ -0,0 +1,47 @@
+name: "hicexplorer_hicpca"
+description: Computes PCA eigenvectors for a Hi-C matrix.
+keywords:
+  - eigenvectors
+  - PCA
+  - hicPCA
+tools:
+  - "hicexplorer":
+      description: "Set of programs to process, analyze and visualize Hi-C and capture Hi-C data"
+      homepage: "https://hicexplorer.readthedocs.io"
+      documentation: "https://hicexplorer.readthedocs.io"
+      tool_dev_url: "https://github.com/deeptools/HiCExplorer"
+      doi: "10.1038/s41467-017-02525-w"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', bin:50000 ]
+  - matrix:
+      type: file
+      description: HiCExplorer matrix in h5 format
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', bin:50000 ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - results:
+      type: file
+      description: Outputs of hicPCA
+  - pca1:
+      type: file
+      description: PCA1 file
+  - pca2:
+      type: file
+      description: PCA2 file
+
+authors:
+  - "@jianhong"

tests/config/pytest_modules.yml

@@ -1550,6 +1550,10 @@ hicap:
   - modules/nf-core/hicap/**
   - tests/modules/nf-core/hicap/**
 
+hicexplorer/hicpca:
+  - modules/nf-core/hicexplorer/hicpca/**
+  - tests/modules/nf-core/hicexplorer/hicpca/**
+
 hifiasm:
   - modules/nf-core/hifiasm/**
   - tests/modules/nf-core/hifiasm/**

tests/modules/nf-core/hicexplorer/hicpca/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HICEXPLORER_HICPCA } from '../../../../../modules/nf-core/hicexplorer/hicpca/main.nf'
+
+workflow test_hicexplorer_hicpca {
+
+    input = [
+        [ id:'test' ], // meta map
+        file('https://github.com/deeptools/HiCExplorer/raw/master/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool', checkIfExists: true)
+    ]
+
+    HICEXPLORER_HICPCA ( input )
+}

tests/modules/nf-core/hicexplorer/hicpca/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/nf-core/hicexplorer/hicpca/test.yml

@@ -0,0 +1,11 @@
+- name: hicexplorer hicpca test_hicexplorer_hicpca
+  command: nextflow run ./tests/modules/nf-core/hicexplorer/hicpca -entry test_hicexplorer_hicpca -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hicexplorer/hicpca/nextflow.config
+  tags:
+    - hicexplorer
+    - hicexplorer/hicpca
+  files:
+    - path: output/hicexplorer/test_pca1.bigwig
+      md5sum: e228fde481bedea641bcd0204bb663a4
+    - path: output/hicexplorer/test_pca2.bigwig
+      md5sum: 109c0d3cc70ecaf3647f3293504a9683
+    - path: output/hicexplorer/versions.yml