Update ichorcna to v0.5.1 and nf-test

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

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-ichorcna=0.3.2
+  - bioconda::r-ichorcna=0.5.1

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

@@ -1,47 +1,85 @@
 process ICHORCNA_CREATEPON {
     label 'process_low'
 
-    // 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--r41hdfd78af_0' :
-        'biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-ichorcna:0.5.1--r43hdfd78af_0' :
+        'biocontainers/r-ichorcna:0.5.1--r43hdfd78af_0' }"
 
     input:
     path wigs
     path gc_wig
     path map_wig
     path centromere
+    path rep_time_wig
+    path exons
 
     output:
-    path "*.rds"        , emit: rds
-    path "*.txt"        , emit: txt
-    path "versions.yml" , emit: versions
+    path "${prefix}*.rds", emit: rds
+    path "${prefix}*.txt", emit: txt
+    path "versions.yml"  , emit: versions
 
     when:
         task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def centro = centromere ? "--centromere ${centromere}" : ''
-    def prefix = task.ext.prefix ?: "PoN"
-    def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def args = task.ext.args     ?: ''
+    prefix = task.ext.prefix ?: "PoN"
+    def map    = map_wig         ? "mapWig='${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='${exons}',"                : ''
+
+    """
+    #!/usr/bin/env Rscript
+    library("ichorCNA")
+    library("yaml")
+
+    write.table(strsplit("${wigs}"," ")[[1]],"filelist.txt", row.names = FALSE, col.names = FALSE)
+
+    createPanelOfNormals(
+        gcWig='${gc_wig}',
+        ${map}
+        ${rep}
+        filelist = "filelist.txt",
+        outfile = "${prefix}",
+        ${exons}
+        ${centro}
+        $args
+    )
+
+    ### Make Versions YAML for NF-Core ###
+    versions = list()
+    versions["r"]        <- paste(R.Version()\$major, R.Version()\$minor, sep=".")
+    versions["ichorCNA"] <- paste(packageVersion("ichorCNA"), sep=".")
+
+    yaml_str <- as.yaml(
+        list(
+            "${task.process}" = versions
+        )
+    )
+    writeLines(yaml_str, file("versions.yml"))
     """
-    echo ${wigs} | tr " " "\\n" > wig_files.txt
-
-    createPanelOfNormals.R \\
-        --filelist wig_files.txt \\
-        --gcWig ${gc_wig} \\
-        --mapWig ${map_wig} \\
-        ${centro} \\
-        ${args} \\
-        --outfile ${prefix}
-
-    rm wig_files.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ichorcna: $VERSION
-    END_VERSIONS
+
+    stub:
+    prefix = task.ext.prefix ?: "PoN"
+    """
+    #!/usr/bin/env Rscript
+    library("yaml")
+
+    file.create("${prefix}.rds")
+    file.create("${prefix}.txt")
+
+    ### Make Versions YAML for NF-Core ###
+    versions = list()
+    versions["r"]        <- paste(R.Version()\$major, R.Version()\$minor, sep=".")
+    versions["ichorCNA"] <- paste(packageVersion("ichorCNA"), sep=".")
+
+    yaml_str <- as.yaml(
+        list(
+            "${task.process}" = versions
+        )
+    )
+    writeLines(yaml_str, file("versions.yml"))
     """
 }

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

@@ -32,6 +32,15 @@ input:
       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:
   - versions:
       type: file

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

@@ -0,0 +1,96 @@
+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)
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.rds[0]).name,
+                    file(process.out.txt[0]).name,
+                    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)
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.rds[0]).name,
+                    file(process.out.txt[0]).name,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = []
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.rds[0]).name,
+                    file(process.out.txt[0]).name,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,44 @@
+{
+    "hg19 - one file": {
+        "content": [
+            "PoN_median.rds",
+            "PoN_median.txt",
+            [
+                "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-08-06T14:23:09.884294332"
+    },
+    "stub": {
+        "content": [
+            "PoN.rds",
+            "PoN.txt",
+            [
+                "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-08-06T14:25:38.594727235"
+    },
+    "hg19 - two files": {
+        "content": [
+            "PoN_median.rds",
+            "PoN_median.txt",
+            [
+                "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-08-06T14:23:29.496424481"
+    }
+}

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=0.5.1