corrected versioning PREPARE_GENOME subworkflow (b9df9166) · Commits · Chaos / Cutandrun

subworkflows/local/prepare_genome.nf

+18 −7

Original line number	Diff line number	Diff line
		@@ -23,11 +23,14 @@ workflow PREPARE_GENOME {
		prepare_tool_indices // list: tools to prepare indices for

		main:
		ch_versions = Channel.empty()

		/*
		* Uncompress genome fasta file if required
		*/
		if (params.fasta.endsWith(".gz")) {
		ch_fasta = GUNZIP_FASTA ( params.fasta ).gunzip
		ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
		} else {
		ch_fasta = file(params.fasta)
		}
		@@ -37,6 +40,7 @@ workflow PREPARE_GENOME {
		*/
		if (params.spikein_fasta.endsWith(".gz")) {
		ch_spikein_fasta = GUNZIP_SPIKEIN_FASTA ( params.spikein_fasta ).gunzip
		ch_versions = ch_versions.mix(GUNZIP_SPIKEIN_FASTA.out.versions)
		} else {
		ch_spikein_fasta = file(params.spikein_fasta)
		}
		@@ -47,6 +51,7 @@ workflow PREPARE_GENOME {
		ch_gtf = Channel.empty()
		if (params.gtf.endsWith(".gz")) {
		ch_gtf = GUNZIP_GTF ( params.gtf ).gunzip
		ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
		} else {
		ch_gtf = file(params.gtf)
		}
		@@ -58,6 +63,7 @@ workflow PREPARE_GENOME {
		if (params.gene_bed){
		if (params.gene_bed.endsWith(".gz")) {
		ch_gene_bed = GUNZIP_BED ( params.gene_bed ).gunzip
		ch_versions = ch_versions.mix(GUNZIP_BED.out.versions)
		} else {
		ch_gene_bed = file(params.gene_bed)
		}
		@@ -67,6 +73,8 @@ workflow PREPARE_GENOME {
		* Create chromosome sizes file
		*/
		ch_chrom_sizes = GET_CHROM_SIZES ( ch_fasta ).sizes
		ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions)


		/*
		* Create chromosome sizes file for spike_in
		@@ -83,22 +91,25 @@ workflow PREPARE_GENOME {
		if (params.bowtie2) {
		if (params.bowtie2.endsWith(".tar.gz")) {
		ch_bt2_index = UNTAR_BT2_INDEX ( params.bowtie2 ).untar
		ch_versions = ch_versions.mix(UNTAR_BT2_INDEX.out.versions)
		} else {
		ch_bt2_index = file(params.bowtie2)
		}
		} else {
		ch_bt2_index = BOWTIE2_BUILD ( ch_fasta ).index
		ch_bt2_versions = BOWTIE2_BUILD.out.versions
		ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
		}

		if (params.spikein_bowtie2) {
		if (params.spikein_bowtie2.endsWith(".tar.gz")) {
		ch_bt2_spikein_index = UNTAR_SPIKEIN_BT2_INDEX ( params.spikein_bowtie2 ).untar
		ch_versions = ch_versions.mix(UNTAR_SPIKEIN_BT2_INDEX.out.versions)
		} else {
		ch_bt2_spikein_index = file(params.spikein_bowtie2)
		}
		} else {
		ch_bt2_spikein_index = BOWTIE2_SPIKEIN_BUILD ( ch_spikein_fasta ).index
		ch_versions = ch_versions.mix(BOWTIE2_SPIKEIN_BUILD.out.versions)
		}
		}

		@@ -110,6 +121,6 @@ workflow PREPARE_GENOME {
		bed = ch_gene_bed // path: genome.bed
		bowtie2_index = ch_bt2_index // path: bt2/index/
		bowtie2_spikein_index = ch_bt2_spikein_index // path: bt2/index/
		bowtie2_versions = ch_bt2_versions // path: *.version.txt
		samtools_versions = GET_CHROM_SIZES.out.versions // path: *.version.txt

		versions = ch_versions // channel: [ versions.yml ]
		}

workflows/cutandrun.nf

+1 −2

Original line number	Diff line number	Diff line
		@@ -368,8 +368,7 @@ workflow CUTANDRUN {
		PREPARE_GENOME (
		prepare_tool_indices
		)
		ch_software_versions = ch_software_versions.mix(PREPARE_GENOME.out.bowtie2_versions)
		ch_software_versions = ch_software_versions.mix(PREPARE_GENOME.out.samtools_versions)
		ch_software_versions = ch_software_versions.mix(PREPARE_GENOME.out.versions)
		}

		/*

Admin message