fix execute parse logs

nf-core · Apr 11, 2024 · 6554b2e · 6554b2e
1 parent e29cfda
commit 6554b2e
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git 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
@@ -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" ) {