diff --git a/modules/sexdeterrmine/main.nf b/modules/sexdeterrmine/main.nf index dd8b5a70..98c72307 100644 --- a/modules/sexdeterrmine/main.nf +++ b/modules/sexdeterrmine/main.nf @@ -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 \\ diff --git a/modules/sexdeterrmine/meta.yml b/modules/sexdeterrmine/meta.yml index 6e24c817..3f56b0ab 100644 --- a/modules/sexdeterrmine/meta.yml +++ b/modules/sexdeterrmine/meta.yml @@ -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: