From c5e83930f603cddfe3fa3e009a75d500f560809c Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 22 Feb 2024 15:06:42 +0000 Subject: [PATCH] Fix thanks to arthur and mahesh --- workflows/smrnaseq.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index e03f90e1..9252fec0 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -87,7 +87,7 @@ workflow NFCORE_SMRNASEQ { .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) mirna_adapters = params.with_umi ? [] : params.fastp_known_mirna_adapters @@ -170,7 +170,7 @@ workflow NFCORE_SMRNASEQ { // SUBWORKFLOW: MIRTRACE // MIRTRACE(ch_mirtrace_inputs) - ch_versions = ch_versions.mix(MIRTRACE.out.versions.ifEmpty(null)) + ch_versions = ch_versions.mix(MIRTRACE.out.versions) // // SUBWORKFLOW: remove contaminants from reads @@ -200,7 +200,7 @@ workflow NFCORE_SMRNASEQ { mirna_gtf, ch_reads_for_mirna ) - ch_versions = ch_versions.mix(MIRNA_QUANT.out.versions.ifEmpty(null)) + ch_versions = ch_versions.mix(MIRNA_QUANT.out.versions) // // GENOME @@ -242,7 +242,7 @@ workflow NFCORE_SMRNASEQ { ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions ) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip.collect{it[1]}.ifEmpty([]))