view

modules/cnvpytor/view/main.nf

@@ -0,0 +1,59 @@
+process CNVPYTOR_VIEW {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(pytor)
+    val bin_sizes
+    val output_format
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf      , optional: true
+    tuple val(meta), path("*.tsv"), emit: tsv      , optional: true
+    tuple val(meta), path("*.xls"), emit: xls      , optional: true
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def output_suffix = output_format ?: 'vcf'
+    """
+
+    python3 <<CODE
+    import cnvpytor,os
+    from pathlib import Path
+    pytor_files = Path.cwd().glob("*.pytor")
+    binsizes = "${bin_sizes}".split(" ")
+    for pytor_file in pytor_files:
+        for binsize in binsizes:
+            file_list = [str(pytor_file)]
+            app = cnvpytor.Viewer(file_list, params={} )
+            outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
+            app.print_filename = outputfile
+            app.bin_size = int(binsize)
+            app.print_calls_file()
+    CODE
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def output_suffix = output_format ?: 'vcf'
+    """
+    touch ${pytor.baseName}.${output_suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
+    END_VERSIONS
+    """
+}

modules/cnvpytor/view/meta.yml

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+name: cnvpytor_view
+description: view function to generate vcfs
+keywords:
+  - cnv calling
+tools:
+  - cnvpytor:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: pytor file containing read depth data
+      pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - partitions:
+      type: file
+      description: pytor file containing partitions of read depth histograms using mean-shift method
+      pattern: "*.{pytor}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@sima-r"