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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Thiseas C. Lamnidis 2022-06-10 11:03:01 +02:00 committed by GitHub
parent 6d04395c3c
commit fe855a1c23
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2 changed files with 7 additions and 7 deletions
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4
modules/sexdeterrmine/main.nf
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@ -9,7 +9,7 @@ process SEXDETERRMINE {
input: input:
tuple val(meta), path(depth) tuple val(meta), path(depth)
path(sample_list_file) path sample_list_file
output: output:
tuple val(meta), path("*.json"), emit: json tuple val(meta), path("*.json"), emit: json
@ -23,7 +23,7 @@ process SEXDETERRMINE {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def sample_list = sample_list_file ? '-f ${sample_list_file}' : '' def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!" if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
""" """
sexdeterrmine \\ sexdeterrmine \\

10
modules/sexdeterrmine/meta.yml
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@ -1,9 +1,10 @@
name: "sexdeterrmine" name: "sexdeterrmine"
description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars. description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
keywords: keywords:
- "sex determination" - sex determination
- "genetic sex" - genetic sex
- "relative coverage" - relative coverage
- ancient dna
tools: tools:
- "sexdeterrmine": - "sexdeterrmine":
description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data." description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
@ -19,10 +20,9 @@ input:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
#
- depth: - depth:
type: file type: file
description: output from samtools depth (with header) description: Output from samtools depth (with header)
pattern: "*" pattern: "*"
output: output: