diff --git a/tests/wrappers/subworkflows/demultiplex/test.yml b/tests/wrappers/subworkflows/demultiplex/test.yml index eb3293c1..e6dc2bf8 100644 --- a/tests/wrappers/subworkflows/demultiplex/test.yml +++ b/tests/wrappers/subworkflows/demultiplex/test.yml @@ -19,7 +19,7 @@ - "wrappers/subworkflows/demultiplex" - name: "test_wrappers_demultiplex_multi_pe" - command: nextflow run ./wrappers/subworkflows/demultiplex/main.nf -c ./tests/config/nextflow.config ---samplesheet ./tests/data/samplesheets/rna-samplesheet.csv --fastqs ./tests/data/fastq_list/multi_pe_fastq.csv + command: nextflow run ./wrappers/subworkflows/demultiplex/main.nf -c ./tests/config/nextflow.config ---samplesheet ./tests/data/samplesheets/clip-samplesheet.csv --fastqs ./tests/data/fastq_list/multi_pe_fastq.csv tags: - "wrappers" - "wrappers/subworkflows" diff --git a/wrappers/subworkflows/demultiplex/main.nf b/wrappers/subworkflows/demultiplex/main.nf index d2b2b685..a7ccca9a 100644 --- a/wrappers/subworkflows/demultiplex/main.nf +++ b/wrappers/subworkflows/demultiplex/main.nf @@ -18,5 +18,5 @@ workflow { // Execute DEMULTIPLEX ( ch_samplesheet, ch_fastqs ) - DEMULTIPLEX.out.fastq | view + //DEMULTIPLEX.out.fastq | view } diff --git a/wrappers/subworkflows/demultiplex/nextflow.config b/wrappers/subworkflows/demultiplex/nextflow.config index 5f9cc07e..057ef2ab 100644 --- a/wrappers/subworkflows/demultiplex/nextflow.config +++ b/wrappers/subworkflows/demultiplex/nextflow.config @@ -17,7 +17,7 @@ process { ext.args = [ "-m5 ${params.fiveprimemismatches}", "-m3 ${params.threeprimemismatches}", - "-a2 ${params.adapter2}", + params.adapter2 ? "-a2 ${params.adapter2}" : '', "-q ${params.phredquality}", "-q5 ${params.phred_quality_5_prime}", "-mt ${params.min_trim}",