diff --git a/modules/nf-core/csvtk/concat/main.nf b/modules/nf-core/csvtk/concat/main.nf index 9f17a9b1b6b4..fdcf8dfb362f 100644 --- a/modules/nf-core/csvtk/concat/main.nf +++ b/modules/nf-core/csvtk/concat/main.nf @@ -13,8 +13,8 @@ process CSVTK_CONCAT { val out_format output: - tuple val(meta), path("${prefix}.${out_extension}"), emit: csv - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.${suffix}"), emit: csv + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -22,9 +22,9 @@ process CSVTK_CONCAT { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: (out_format == 'tsv' ? 'tsv' : 'csv') def delimiter = in_format == "tsv" ? "\t" : (in_format == "csv" ? "," : in_format) def out_delimiter = out_format == "tsv" ? "\t" : (out_format == "csv" ? "," : out_format) - out_extension = out_format == "tsv" ? 'tsv' : 'csv' """ csvtk \\ concat \\ @@ -32,7 +32,7 @@ process CSVTK_CONCAT { --num-cpus $task.cpus \\ --delimiter "${delimiter}" \\ --out-delimiter "${out_delimiter}" \\ - --out-file ${prefix}.${out_extension} \\ + --out-file ${prefix}.${suffix} \\ $csv cat <<-END_VERSIONS > versions.yml @@ -43,9 +43,9 @@ process CSVTK_CONCAT { stub: prefix = task.ext.prefix ?: "${meta.id}" - out_extension = out_format == "tsv" ? 'tsv' : 'csv' + suffix = task.ext.suffix ?: (out_format == 'tsv' ? 'tsv' : 'csv') """ - touch ${prefix}.${out_extension} + touch ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml index 37497b3122c5..a833b0bf24e8 100644 --- a/modules/nf-core/csvtk/concat/meta.yml +++ b/modules/nf-core/csvtk/concat/meta.yml @@ -40,7 +40,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - ${prefix}.${out_extension}: + - ${prefix}.${suffix}: type: file description: Concatenated CSV/TSV file pattern: "*.{csv,tsv}"