add freec2circos script (#1454)

* add freec2circos script

* remove todo statements

modules/controlfreec/freec2circos/main.nf

@@ -0,0 +1,31 @@
+process CONTROLFREEC_FREEC2CIRCOS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
+        'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
+
+    input:
+    tuple val(meta), path(ratio)
+
+    output:
+    tuple val(meta), path("*.circos.txt"), emit: circos
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    freec2circos.pl -f ${ratio} ${args} > ${prefix}.circos.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
+}

modules/controlfreec/freec2circos/meta.yml

@@ -0,0 +1,45 @@
+name: controlfreec_freec2circos
+description: Format Freec output to circos input format
+keywords:
+  - cna
+  - cnv
+  - somatic
+  - single
+  - tumor-only
+tools:
+  - controlfreec:
+      description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
+      homepage: http://boevalab.inf.ethz.ch/FREEC
+      documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
+      tool_dev_url: https://github.com/BoevaLab/FREEC/
+      doi: "10.1093/bioinformatics/btq635"
+      licence: ["GPL >=2"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - ratio:
+      type: file
+      description: ratio file generated by FREEC
+      pattern: "*.ratio.txt"
+
+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"
+  - circos:
+      type: file
+      description: Txt file
+      pattern: "*.circos.txt"
+
+authors:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -431,6 +431,10 @@ controlfreec/freec2bed:
   - modules/controlfreec/freec2bed/**
   - tests/modules/controlfreec/freec2bed/**
 
+controlfreec/freec2circos:
+  - modules/controlfreec/freec2circos/**
+  - tests/modules/controlfreec/freec2circos/**
+
 controlfreec/makegraph:
   - modules/controlfreec/makegraph/**
   - tests/modules/controlfreec/makegraph/**

tests/modules/controlfreec/freec2circos/main.nf

@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_FREEC2CIRCOS } from '../../../../modules/controlfreec/freec2circos/main.nf'
+include { CONTROLFREEC_FREEC     } from '../../../../modules/controlfreec/freec/main.nf'
+include { UNTAR                  } from '../../../../modules/untar/main.nf'
+
+workflow test_controlfreec_freec2circos {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
+}

tests/modules/controlfreec/freec2circos/nextflow.config

@@ -0,0 +1,27 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:CONTROLFREEC_FREEC{
+        ext.args = { [
+                    "sample":[
+                        inputformat: 'pileup',
+                        mateorientation: 'FR'
+                    ],
+                    "general" :[
+                        bedgraphoutput: "TRUE",
+                        noisydata: "TRUE",
+                        minexpectedgc: "0",
+                        readcountthreshold: "1",
+                        sex: meta.sex,
+                        window: "10",
+                        ],
+                    "control":[
+                        inputformat: "pileup",
+                        mateorientation: "FR"
+                    ]
+                    ]
+        }
+    }
+
+}

tests/modules/controlfreec/freec2circos/test.yml

@@ -0,0 +1,8 @@
+- name: controlfreec freec2circos test_controlfreec_freec2circos
+  command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos -c tests/config/nextflow.config
+  tags:
+    - controlfreec
+    - controlfreec/freec2circos
+  files:
+    - path: output/controlfreec/test.circos.txt
+      md5sum: 19cf35f2c36b46f717dc8342b8a5a645