Allow samplesheets with no R1 or R2 (#12)

BCCDC-PHL · Dec 22, 2023 · 1987736 · 1987736
1 parent 4dedcc2
commit 1987736
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/main.nf b/main.nf
@@ -33,7 +33,7 @@ workflow {
     ch_pipeline_provenance = pipeline_provenance(ch_pipeline_name.combine(ch_pipeline_version))
 
     if (params.samplesheet_input != 'NO_FILE') {
-	ch_illumina_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }
+	ch_illumina_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['R1'], it['R2']] }.filter{ it -> it[1] != null || it[2] != null }
 	ch_nanopore_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['LONG']] }.filter{ it -> it[1] != null }
 	ch_ref = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], it['REF']] }
     } else {

diff --git a/nextflow.config b/nextflow.config
@@ -4,7 +4,7 @@ manifest {
     description = 'Alignment and variant calling pipeline'
     mainScript = 'main.nf'
     nextflowVersion = '>=20.01.0'
-    version = '0.1.5'
+    version = '0.1.6'
 }
 
 params {