From 489312afc7ecb47c33898856199aafb647deb050 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Sun, 19 May 2024 10:30:20 +0100 Subject: [PATCH] Cleaned up the busco_db parameter --- subworkflows/local/busco_diamond_blastp.nf | 2 +- workflows/blobtoolkit.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/busco_diamond_blastp.nf b/subworkflows/local/busco_diamond_blastp.nf index 2efb2728..bd50a37a 100644 --- a/subworkflows/local/busco_diamond_blastp.nf +++ b/subworkflows/local/busco_diamond_blastp.nf @@ -70,7 +70,7 @@ workflow BUSCO_DIAMOND { ch_fasta_with_lineage, "genome", ch_fasta_with_lineage.map { it[0].lineage_name }, - busco_db.collect().ifEmpty([]), + busco_db, [], ) ch_versions = ch_versions.mix ( BUSCO.out.versions.first() ) diff --git a/workflows/blobtoolkit.nf b/workflows/blobtoolkit.nf index 0b6432d9..37f27f7b 100644 --- a/workflows/blobtoolkit.nf +++ b/workflows/blobtoolkit.nf @@ -31,7 +31,7 @@ if (params.taxdump) { ch_taxdump = file(params.taxdump) } else { exit 1, 'NCBI T if (params.fetchngs_samplesheet && !params.align) { exit 1, '--align not specified, even though the input samplesheet is a nf-core/fetchngs one - i.e has fastq files!' } // Create channel for optional parameters -if (params.busco_db) { ch_busco_db = Channel.fromPath(params.busco_db) } else { ch_busco_db = Channel.empty() } +if (params.busco_db) { ch_busco_db = Channel.fromPath(params.busco_db).first() } else { ch_busco_db = Channel.value([]) } if (params.yaml) { ch_yaml = Channel.fromPath(params.yaml) } else { ch_yaml = Channel.empty() } if (params.yaml && params.accession) { exit 1, '--yaml cannot be provided at the same time as --accession !' } if (!params.yaml && !params.accession) { exit 1, '--yaml and --accession are both mising. Pick one !' }