Excluding undetermined indices from search pattern

ikmb · Nov 27, 2023 · 55857ab · 55857ab
1 parent 6d96083
commit 55857ab
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/main.nf b/main.nf
@@ -77,7 +77,7 @@ log.info "Target folder:		${params.folder}"
 
 // Get list of all project folders
 
-reads = Channel.fromPath("${demux_folder}/[A-Z][A-Za-z]*_*[0-9]/*_R*_001.fastq.gz")
+reads = Channel.fromPath("${demux_folder}/[A-Z][A-Za-z]*_*/*_R*_001.fastq.gz").filter { !it.toString().contains("Undetermined") }  
 //diagx_reads = Channel.fromPath("${demux_folder}/NGS_Diagnostik-Exome/*_001.fastq.gz")
 
 

diff --git a/modules/fastp.nf b/modules/fastp.nf
@@ -8,7 +8,7 @@ process FASTP {
 	tuple val(project),val(lib),path(reads)
 
 	output:
-	tuple val(project),val(lib),path(ltrim),path(rtrim), emit: reads
+	tuple val(project),val(lib),path(ltrim),path(rtrim), optional: true, emit: reads
 	path(json), emit: json
 
 	script:

diff --git a/nextflow.config b/nextflow.config
@@ -17,7 +17,7 @@ params {
 }
 
 manifest {
-	version = "1.7.2"
+	version = "1.7.3"
 	description = "NGS QC Pipeline"
 	author = "Marc P. Hoeppner"
 	homePage = "https://github.com/ikmb/ngs-qc"