From 5b1cca1925de1e6aeba97661d7c47d2a94122805 Mon Sep 17 00:00:00 2001 From: jvfe Date: Tue, 9 Apr 2024 12:58:45 -0300 Subject: [PATCH] hotfix: Remove reference requirement when skip_alignment is on Signed-off-by: jvfe --- workflows/euryale.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/euryale.nf b/workflows/euryale.nf index 7f899ab..7b9f06c 100644 --- a/workflows/euryale.nf +++ b/workflows/euryale.nf @@ -72,7 +72,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft def multiqc_report = [] workflow EURYALE { - if (params.reference_fasta == null && params.diamond_db == null) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' } + if (params.reference_fasta == null && params.diamond_db == null && params.skip_alignment == false) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' } if (params.run_kaiju == true && params.kaiju_db == null) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'} if (params.run_kraken2 == true && params.kraken2_db == null) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'} if (params.host_fasta == null && params.bowtie2_db == null && params.skip_host_removal == false) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}