Module: ichorcna/run updated to v0.5.0

modules/nf-core/ichorcna/createpon/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-ichorcna=0.3.2
+  - bioconda::r-ichorcna=0.5.0

modules/nf-core/ichorcna/createpon/tests/main.nf.test

@@ -0,0 +1,67 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test ichorcna/createpon
+nextflow_process {
+
+    name "Test Process ICHORCNA_CREATEPON"
+    script "../main.nf"
+    process "ICHORCNA_CREATEPON"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ichorcna"
+    tag "ichorcna/createpon"
+
+    test("hg19 - one file") {
+
+        when {
+            process {
+                """
+                input[0] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true)
+                input[1] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+                input[2] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+                input[3] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.rds.get(0)).name).match("PoN_median.rds") },
+                { assert snapshot(file(process.out.txt.get(0)).name).match("PoN_median.txt") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+
+    test("hg19 - two files") {
+
+        when {
+            process {
+                """
+                input[0] = [ file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true),
+                            file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true)
+                            ]
+
+                input[1] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true)
+                input[2] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true)
+                input[3] = file("https://raw.githubusercontent.com/gavinhalab/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.rds.get(0)).name).match("PoN_median.rds") },
+                { assert snapshot(file(process.out.txt.get(0)).name).match("PoN_median.txt") },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+
+}

modules/nf-core/ichorcna/createpon/tests/tags.yml

@@ -0,0 +1,2 @@
+ichorcna/createpon:
+  - "modules/nf-core/ichorcna/createpon/**"

modules/nf-core/ichorcna/run/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-ichorcna=0.3.2
+  - bioconda::r-ichorcna=0.5.0

modules/nf-core/ichorcna/run/main.nf

@@ -5,47 +5,68 @@ process ICHORCNA_RUN {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--pl5321r42hdfd78af_2' :
-        'biocontainers/r-ichorcna:0.3.2--pl5321r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-ichorcna:0.5.0--pl5321r42hdfd78af_0' :
+        'biocontainers/r-ichorcna:0.5.0--pl5321r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(wig)
     path gc_wig
     path map_wig
-    path panel_of_normals
+    path normal_wig
+    path normal_background
     path centromere
+    path rep_time_wig
+    path exons
 
     output:
-    tuple val(meta), path("*.cna.seg")    , emit: cna_seg
-    tuple val(meta), path("*.params.txt") , emit: ichorcna_params
-    path "*genomeWide.pdf"                , emit: genome_plot
-    path "versions.yml"                   , emit: versions
+    tuple val(meta), path("**.cna.seg")    , emit: cna_seg
+    tuple val(meta), path("**.params.txt") , emit: ichorcna_params
+    tuple val(meta), path("**.pdf")        , emit: genome_plot
+    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 pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : ''
-    def centro = centromere ? "--centromere ${centromere}" : ''
-    def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def args = task.ext.args       ?: ''
+    def prefix = task.ext.prefix   ?: "${meta.id}"
+    def norm   = normal_wig        ? "normal_wig='${normal_wig}',"          : 'normal_wig=NULL,'
+    def pon    = normal_background ? "normal_panel='${normal_background}'," : 'normal_panel=NULL,'
+    def map    = map_wig           ? "mapWig='${map_wig}',"                 : 'mapWig=NULL,'
+    def centro = centromere        ? "centromere='${centromere}',"          : ''
+    def rep    = rep_time_wig      ? "repTimeWig='${rep_time_wig}',"        : 'repTimeWig=NULL,'
+    def exons  = exons             ? "exons.bed='${exons}',"                : ''
     """
-    runIchorCNA.R \\
-        $args \\
-        --WIG ${wig} \\
-        --id ${prefix} \\
-        --gcWig ${gc_wig} \\
-        --mapWig ${map_wig} \\
-        ${pon} \\
-        ${centro} \\
-        --outDir .
-
-    cp */*genomeWide.pdf .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ichorcna: $VERSION
-    END_VERSIONS
+    #!/usr/bin/env Rscript
+    library("ichorCNA")
+    library("yaml")
+
+    run_ichorCNA(
+        tumor_wig='${wig}',
+        id='${prefix}',
+        cores=${task.cpus},
+        gcWig='${gc_wig}',
+        $norm
+        $pon
+        $map
+        $centro
+        $rep
+        $exons
+        $args
+        outDir="."
+    )
+
+
+    ### Make Versions YAML for NF-Core ###
+    versions = list()
+    versions["r"]        <- paste(R.Version()\$major, R.Version()\$minor, sep=".")
+    versions["ichorCNA"] <- paste(packageVersion("ichorCNA"), sep=".")
+
+    yaml_str <- as.yaml(
+        list(
+            "${task.process}" = versions
+        )
+    )
+    writeLines(yaml_str, file("versions.yml"))
     """
 }

modules/nf-core/ichorcna/run/meta.yml

@@ -20,49 +20,78 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test']
+
   - wig:
       type: file
       description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window
       pattern: "*.{wig}"
+
   - gc_wig:
       type: file
       description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
       pattern: "*.{wig}"
+
   - map_wig:
       type: file
       description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
       pattern: "*.{wig}"
-  - panel_of_normals:
+
+  - normal_wig:
+      type: file
+      description: hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window
+      pattern: "*.{wig}"
+
+  - normal_background:
       type: file
       description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.
       pattern: "*.{rds}"
+
   - centromere:
       type: file
       description: Text file giving centromere locations of each genome, to exclude these windows
       pattern: "*.{txt}"
+
+  - rep_time_wig:
+      type: file
+      description: Replication/timing .wig file.
+      pattern: "*.{wig}"
+
+  - exons:
+      type: file
+      description: BED file for exon regions to annotate CNA regions.
+      pattern: "*.{bed}"
+
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test']
+
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+
   - cna_seg:
       type: file
       description: Predicted copy number variation per segment
       pattern: "*.{cng.seg}"
+
   - ichorcna_params:
       type: file
       description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc
       pattern: "*.{params.txt}"
+
   - genome_plot:
       type: file
       description: A plot with the best-fit genome-wide CNV data
       pattern: "*.{genomeWide.pdf}"
+
 authors:
   - "@sppearce"
+  - "@adamrtalbot"
+
 maintainers:
   - "@sppearce"
+  - "@adamrtalbot"