Updated bedtools sort (b39ae0ee) · Commits · Chaos / Cutandrun

modules/nf-core/modules/bedtools/sort/main.nf

+6 −5

Original line number	Diff line number	Diff line
		@@ -19,10 +19,11 @@ process BEDTOOLS_SORT {
		}

		input:
		tuple val(meta), path(bed)
		tuple val(meta), path(intervals)
		val extension

		output:
		tuple val(meta), path('*.bed'), emit: bed
		tuple val(meta), path("*.${extension}"), emit: sorted
		path "versions.yml" , emit: versions

		script:
		@@ -30,9 +31,9 @@ process BEDTOOLS_SORT {
		"""
		bedtools \\
		sort \\
		-i $bed \\
		-i $intervals \\
		$options.args \\
		> ${prefix}.bed
		> ${prefix}.${extension}

		cat <<-END_VERSIONS > versions.yml
		${getProcessName(task.process)}:

+13 −6

Original line number	Diff line number	Diff line
		@@ -15,20 +15,26 @@ input:
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- bed:
		- intervals:
		type: file
		description: Input BED file
		pattern: "*.{bed}"
		description: BED/BEDGRAPH
		pattern: "*.{bed\|bedGraph}"

		- extension:
		type: string
		description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
		output:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- bed:

		- sorted:
		type: file
		description: Sorted BED file
		pattern: "*.{bed}"
		description: Sorted output file
		pattern: "*.${extension}"

		- versions:
		type: file
		description: File containing software versions
		@@ -37,3 +43,4 @@ authors:
		- "@Emiller88"
		- "@sruthipsuresh"
		- "@drpatelh"
		- "@chris-cheshire"