From e1963fb4fec61c34de251f73415d8621461cef7a Mon Sep 17 00:00:00 2001 From: Anders Jemt Date: Fri, 12 Jan 2024 17:32:31 +0100 Subject: [PATCH] Fix for getting chr sizes when fai is given --- subworkflows/local/prepare_references.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 9752b3f3..e91494c1 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -48,10 +48,10 @@ workflow PREPARE_REFERENCES { SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]) GATK_SD(ch_genome_fasta) - GET_CHROM_SIZES( SAMTOOLS_FAIDX_GENOME.out.fai ) + ch_fai = Channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect() + GET_CHROM_SIZES( ch_fai ) // MT indices - ch_fai = Channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect() SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) ch_mt_fasta_in = Channel.empty().mix(ch_mt_fasta, SAMTOOLS_EXTRACT_MT.out.fa).collect() SAMTOOLS_FAIDX_MT_SHIFT(ch_mt_fasta_in, [[],[]])