fix

nf-core · Feb 14, 2025 · 68b686d · 68b686d
1 parent 0e3a3ec
commit 68b686d
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Showing 2 changed files with 5 additions and 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
@@ -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
@@ -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)