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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2 changed files with 7 additions and 7 deletions
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@ -9,7 +9,7 @@ process SEXDETERRMINE {
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input:
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tuple val(meta), path(depth)
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path(sample_list_file)
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path sample_list_file
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output:
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tuple val(meta), path("*.json"), emit: json
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@ -23,7 +23,7 @@ process SEXDETERRMINE {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
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if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
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"""
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sexdeterrmine \\
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@ -1,9 +1,10 @@
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name: "sexdeterrmine"
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description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
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keywords:
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- "sex determination"
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- "genetic sex"
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- "relative coverage"
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- sex determination
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- genetic sex
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- relative coverage
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- ancient dna
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tools:
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- "sexdeterrmine":
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description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
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@ -19,10 +20,9 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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#
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- depth:
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type: file
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description: output from samtools depth (with header)
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description: Output from samtools depth (with header)
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pattern: "*"
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output:
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