Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This commit is contained in:
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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@ -9,7 +9,7 @@ process SEXDETERRMINE {
input:
tuple val(meta), path(depth)
path(sample_list_file)
path sample_list_file
output:
tuple val(meta), path("*.json"), emit: json
@ -23,7 +23,7 @@ process SEXDETERRMINE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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 \\

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@ -1,9 +1,10 @@
name: "sexdeterrmine"
description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
keywords:
- "sex determination"
- "genetic sex"
- "relative coverage"
- sex determination
- genetic sex
- relative coverage
- ancient dna
tools:
- "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."
@ -19,10 +20,9 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
#
- depth:
type: file
description: output from samtools depth (with header)
description: Output from samtools depth (with header)
pattern: "*"
output: