From c28f08dba890f1002b88eeddd31e8eb0c5513604 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Mon, 21 Aug 2023 14:10:37 +0200 Subject: [PATCH] try to fix samtools/faidx --- subworkflows/local/community.nf | 2 +- subworkflows/local/input_check.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/community.nf b/subworkflows/local/community.nf index a843a1b9..e292e110 100644 --- a/subworkflows/local/community.nf +++ b/subworkflows/local/community.nf @@ -45,7 +45,7 @@ workflow COMMUNITY { TABIX_BGZIP(EXTRACT_COMMUNITIES.out.community_fasta) ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) - SAMTOOLS_FAIDX(TABIX_BGZIP.out.output) + SAMTOOLS_FAIDX(TABIX_BGZIP.out.output, [[],[]]) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) emit: diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 6be6c7a1..a0cfeb56 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -28,7 +28,7 @@ workflow INPUT_CHECK { // TODO We want to check, if the input file was actually compressed with bgzip with the upcoming grabix module. // For now we assume it was bgzip. If not WFMASH will complain instantly anyhow. if (!fai_path.exists() || !gzi_path.exists()) { // the assumption is that none of these files exist if only one does not exist - SAMTOOLS_FAIDX(meta_fasta) + SAMTOOLS_FAIDX(meta_fasta, [[],[]]) fai = SAMTOOLS_FAIDX.out.fai gzi = SAMTOOLS_FAIDX.out.gzi ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) @@ -50,7 +50,7 @@ workflow INPUT_CHECK { meta_fasta = tuple([ id:fasta_file_name ], fasta) TABIX_BGZIP(meta_fasta) ch_fasta = TABIX_BGZIP.out.output - SAMTOOLS_FAIDX(ch_fasta) + SAMTOOLS_FAIDX(ch_fasta, [[],[]]) gzi = SAMTOOLS_FAIDX.out.gzi fai = SAMTOOLS_FAIDX.out.fai ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)