Merge branch 'char-dev' into dev (90a8969f) · Commits · Chaos / Cutandrun

lib/WorkflowMain.groovy

+6 −2

Original line number	Diff line number	Diff line
		@@ -83,7 +83,9 @@ class WorkflowMain {
		//
		public static String getGenomeAttribute(params, attribute) {
		def val = ''
		if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.genomes[ params.genome ].containsKey(attribute)) {
		val = params.genomes[ params.genome ][ attribute ]
		}
		@@ -96,7 +98,9 @@ class WorkflowMain {
		//
		public static String getGenomeAttributeSpikeIn(params, attribute) {
		def val = ''
		if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.genomes[ params.spikein_genome ].containsKey(attribute)) {
		val = params.genomes[ params.spikein_genome ][ attribute ]
		}

main.nf

+16 −7

Original line number	Diff line number	Diff line
		@@ -17,11 +17,18 @@ nextflow.enable.dsl = 2
		========================================================================================
		*/

		params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
		params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
		params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
		params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
		params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		if (!params.fasta) {
		params.bowtie2 = params.bowtie2 ?: WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		}
		params.fasta = params.fasta ?: WorkflowMain.getGenomeAttribute(params, 'fasta')
		params.gtf = params.gtf ?: WorkflowMain.getGenomeAttribute(params, 'gtf')
		params.gene_bed = params.gene_bed ?: WorkflowMain.getGenomeAttribute(params, 'bed12')
		params.blacklist = params.blacklist ?: WorkflowMain.getGenomeAttribute(params, 'blacklist')

		// params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
		// params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
		// params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
		// params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')

		/*
		========================================================================================
		@@ -29,8 +36,10 @@ params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
		========================================================================================
		*/

		params.spikein_fasta = WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')
		params.spikein_bowtie2 = WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
		if (!params.spikein_fasta) {
		params.spikein_bowtie2 = params.spikein_bowtie2 ?: WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
		}
		params.spikein_fasta = params.spikein_fasta ?: WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')

		/*
		========================================================================================

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