From 6554b2ed70a607c44623ad0fa7cdc1812a7a841d Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 11 Apr 2024 12:55:55 -0400 Subject: [PATCH] fix execute parse logs --- .../local/repertoire_analysis_reporting.nf | 2 +- workflows/airrflow.nf | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/repertoire_analysis_reporting.nf b/subworkflows/local/repertoire_analysis_reporting.nf index cbcf7456..2a796751 100644 --- a/subworkflows/local/repertoire_analysis_reporting.nf +++ b/subworkflows/local/repertoire_analysis_reporting.nf @@ -30,7 +30,7 @@ workflow REPERTOIRE_ANALYSIS_REPORTING { main: ch_versions = Channel.empty() - if (params.mode == "fastq" && !params.library_generation_method in ["sc_10x_genomics"]) { + if (params.mode == "fastq" && params.library_generation_method != "sc_10x_genomics") { PARSE_LOGS( ch_presto_filterseq_logs, ch_presto_maskprimers_logs, diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf index 41a96d90..6b2eb589 100644 --- a/workflows/airrflow.nf +++ b/workflows/airrflow.nf @@ -119,15 +119,15 @@ workflow AIRRFLOW { ch_fastp_json = SEQUENCE_ASSEMBLY.out.fastp_reads_json ch_fastqc_postassembly_mqc = SEQUENCE_ASSEMBLY.out.fastqc_postassembly ch_validated_samplesheet = SEQUENCE_ASSEMBLY.out.samplesheet.collect() - ch_presto_filterseq_logs = SEQUENCE_ASSEMBLY.out.presto_filterseq_logs - ch_presto_maskprimers_logs = SEQUENCE_ASSEMBLY.out.presto_maskprimers_logs - ch_presto_pairseq_logs = SEQUENCE_ASSEMBLY.out.presto_pairseq_logs - ch_presto_clustersets_logs = SEQUENCE_ASSEMBLY.out.presto_clustersets_logs - ch_presto_buildconsensus_logs = SEQUENCE_ASSEMBLY.out.presto_buildconsensus_logs - ch_presto_postconsensus_pairseq_logs = SEQUENCE_ASSEMBLY.out.presto_postconsensus_pairseq_logs - ch_presto_assemblepairs_logs = SEQUENCE_ASSEMBLY.out.presto_assemblepairs_logs - ch_presto_collapseseq_logs = SEQUENCE_ASSEMBLY.out.presto_collapseseq_logs - ch_presto_splitseq_logs = SEQUENCE_ASSEMBLY.out.presto_splitseq_logs + ch_presto_filterseq_logs = SEQUENCE_ASSEMBLY.out.presto_filterseq_logs.ifEmpty([]) + ch_presto_maskprimers_logs = SEQUENCE_ASSEMBLY.out.presto_maskprimers_logs.ifEmpty([]) + ch_presto_pairseq_logs = SEQUENCE_ASSEMBLY.out.presto_pairseq_logs.ifEmpty([]) + ch_presto_clustersets_logs = SEQUENCE_ASSEMBLY.out.presto_clustersets_logs.ifEmpty([]) + ch_presto_buildconsensus_logs = SEQUENCE_ASSEMBLY.out.presto_buildconsensus_logs.ifEmpty([]) + ch_presto_postconsensus_pairseq_logs = SEQUENCE_ASSEMBLY.out.presto_postconsensus_pairseq_logs.ifEmpty([]) + ch_presto_assemblepairs_logs = SEQUENCE_ASSEMBLY.out.presto_assemblepairs_logs.ifEmpty([]) + ch_presto_collapseseq_logs = SEQUENCE_ASSEMBLY.out.presto_collapseseq_logs.ifEmpty([]) + ch_presto_splitseq_logs = SEQUENCE_ASSEMBLY.out.presto_splitseq_logs.ifEmpty([]) } } else if ( params.mode == "assembled" ) {