From 68b686d48181ae508c9f983faf23beadbc875fec Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Fri, 14 Feb 2025 08:27:45 +0000 Subject: [PATCH] fix --- .../nf-core/fastq_create_umi_consensus_fgbio/main.nf | 2 +- tests/modules/nf-core/graphtyper/genotype/main.nf | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf index 1138f3f3bd6..175a2bda9e6 100644 --- a/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf +++ b/subworkflows/nf-core/fastq_create_umi_consensus_fgbio/main.nf @@ -79,7 +79,7 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO { // appropriately tagged interleaved FASTQ reads are mapped to the reference // the aligner should be set with the following parameters "-p -K 150000000 -Y" // to be configured in ext.args of your config - BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, false ) + BWAMEM1_MEM_PRE ( BAM2FASTQ_PRE.out.fastq, bwaindex, [[],[]], false ) ch_versions = ch_versions.mix(BWAMEM1_MEM_PRE.out.versions) aligned_bam = aligned_bam.mix(BWAMEM1_MEM_PRE.out.bam) } else { diff --git a/tests/modules/nf-core/graphtyper/genotype/main.nf b/tests/modules/nf-core/graphtyper/genotype/main.nf index 90270f66b8b..d93f8c06f41 100644 --- a/tests/modules/nf-core/graphtyper/genotype/main.nf +++ b/tests/modules/nf-core/graphtyper/genotype/main.nf @@ -35,7 +35,10 @@ workflow test_graphtyper_genotype_multi { file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) ] ] ) - reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true).map { it -> [ [ 'id': it.simpleName], it ] } + reference = Channel.of([ + [ id: 'test_genome'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ]) ref_with_meta = [ [ id: 'ref' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ref_index = [ [ id: 'ref_index' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)] region = file(params.test_data['sarscov2']['genome']['regions_txt'], checkIfExists: true)