add makegraph script (#1452)

* add makegraph script

* allow renaming of output files

* allow renaming of output files

modules/controlfreec/assesssignificance/main.nf

@@ -11,7 +11,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
     tuple val(meta), path(cnvs), path(ratio)
 
     output:
-    tuple val(meta), path("*.p.value.txt"), emit: bam
+    tuple val(meta), path("*.p.value.txt"), emit: p_value_txt
     path "versions.yml"                   , emit: versions
 
     when:
@@ -19,9 +19,12 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
 
+    mv *.p.value.txt ${prefix}.p.value.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )

modules/controlfreec/makegraph/main.nf

@@ -0,0 +1,40 @@
+process CONTROLFREEC_MAKEGRAPH {
+    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), path(baf)
+
+    output:
+    tuple val(meta), path("*_BAF.png")       , emit: png_baf
+    tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
+    tuple val(meta), path("*_ratio.png")     , emit: png_ratio
+
+    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}"
+    def baf = baf ?: ""
+    """
+    cat /usr/local/bin/makeGraph.R | R --slave --args ${args} ${ratio} ${baf}
+
+    mv *_BAF.txt.png ${prefix}_BAF.png
+    mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
+    mv *_ratio.txt.png ${prefix}_ratio.png
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
+}

modules/controlfreec/makegraph/meta.yml

@@ -0,0 +1,58 @@
+name: controlfreec_makegraph
+description: Plot Freec output
+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:
+  # Only when we have meta
+  - 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"
+  - baf:
+      type: file
+      description: .BAF file generated by FREEC
+      pattern: "*.BAF"
+
+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"
+  - png_baf:
+      type: file
+      description: Image of BAF plot
+      pattern: "*_BAF.png"
+  - png_ratio_log2:
+      type: file
+      description: Image of ratio log2 plot
+      pattern: "*_ratio.log2.png"
+  - png_ratio:
+      type: file
+      description: Image of ratio plot
+      pattern: "*_ratio.png"
+
+authors:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

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

tests/modules/controlfreec/assesssignificance/test.yml

@@ -4,7 +4,7 @@
     - controlfreec/assesssignificance
     - controlfreec
   files:
-    - path: output/controlfreec/test2.mpileup.gz_CNVs.p.value.txt
+    - path: output/controlfreec/test.p.value.txt
       md5sum: 44e23b916535fbc1a3f47b57fad292df
     - path: output/controlfreec/versions.yml
       md5sum: 0aa42fed10d61e4570fe1e0e83ffe932

tests/modules/controlfreec/makegraph/main.nf

@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/controlfreec/makegraph/main.nf'
+include { CONTROLFREEC_FREEC     } from '../../../../modules/controlfreec/freec/main.nf'
+include { UNTAR                  } from '../../../../modules/untar/main.nf'
+
+workflow test_controlfreec_makegraph {
+
+    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,
+                        []
+                        )
+
+    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
+    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
+}

tests/modules/controlfreec/makegraph/nextflow.config

@@ -0,0 +1,30 @@
+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"
+                    ]
+                    ]
+        }
+    }
+
+    withName:CONTROLFREEC_MAKEGRAPH {
+        ext.args = "2"
+    }
+}

tests/modules/controlfreec/makegraph/test.yml

@@ -0,0 +1,12 @@
+- name: controlfreec makegraph test_controlfreec_makegraph
+  command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config
+  tags:
+    - controlfreec
+    - controlfreec/makegraph
+  files:
+    - path: output/controlfreec/test_BAF.png
+      md5sum: f9d977839e09c7e2472d970bd4aa834c
+    - path: output/controlfreec/test_ratio.log2.png
+      md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
+    - path: output/controlfreec/test_ratio.png
+      md5sum: 1435b29536b3b1555b4c423f8f4fb000