From 93f70c2957305631c67dbc834bd157c932db6d25 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 19 Oct 2022 08:49:26 +0100 Subject: [PATCH] bugfix: only use the CLI params if the samplesheet is not provided --- subworkflows/local/params_check.nf | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/params_check.nf b/subworkflows/local/params_check.nf index 047c1f1..50dfc41 100644 --- a/subworkflows/local/params_check.nf +++ b/subworkflows/local/params_check.nf @@ -35,11 +35,12 @@ workflow PARAMS_CHECK { ] } .set { ch_inputs } - ch_versions = ch_versions.mix(SAMPLESHEET_CHECK.out.versions.first()) - } + ch_versions = ch_versions.mix(SAMPLESHEET_CHECK.out.versions) - // Add the other input channel in, as it's expected to have all the parameters in the right order - ch_inputs = ch_inputs.mix(cli_params) + } else { + // Add the other input channel in, as it's expected to have all the parameters in the right order + ch_inputs = ch_inputs.mix(cli_params) + } emit: ensembl_params = ch_inputs // tuple(analysis_dir, ensembl_species_name, assembly_accession, geneset_version)