added less stringend barcoding

modules/filter_fastq_by_length.nf

@@ -13,8 +13,8 @@ process filter_fastq_by_length {
                 awk -F"\\t" 'length(\$2)  <= 1500' | sed 's/\\t/\\n/g' | gzip > "${name}_filtered.fastq.gz"
         ;;
         *.fastq)
-            cat ${reads} | paste - - - - | awk -F"\\t" 'length(\$2)  >= 1000' | sed 's/\\t/\\n/g' |\
-            awk -F"\\t" 'length(\$2)  <= 1300' | sed 's/\\t/\\n/g' | gzip > "${name}_filtered.fastq.gz"
+            cat ${reads} | paste - - - - | awk -F"\\t" 'length(\$2)  >= 250' | sed 's/\\t/\\n/g' |\
+            awk -F"\\t" 'length(\$2)  <= 1500' | sed 's/\\t/\\n/g' | gzip > "${name}_filtered.fastq.gz"
         ;;
     esac
 

modules/guppy.nf

@@ -20,7 +20,7 @@ process guppy_gpu {
         mkdir -p fastq_tmp/
         cp fastq/*.txt fastq_tmp
         """
-        else if (!params.single)
+        if (!params.single && !params.one_end)
         """
         guppy_basecaller -c dna_r9.4.1_450bps_hac.cfg -i ${dir} -s fastq_tmp -x auto -r
         guppy_barcoder --require_barcodes_both_ends -i fastq_tmp -s fastq --arrangements_files "barcode_arrs_nb12.cfg barcode_arrs_nb24.cfg"
@@ -29,6 +29,17 @@ process guppy_gpu {
             find -L \${barcodes} -name '*.fastq' -exec cat {} + | gzip > \${barcodes##*/}.fastq.gz
         done
 
+        cp fastq/*.txt fastq_tmp
+        """
+        else if (!params.single && params.one_end)
+        """
+        guppy_basecaller -c dna_r9.4.1_450bps_hac.cfg -i ${dir} -s fastq_tmp -x auto -r
+        guppy_barcoder -i fastq_tmp -s fastq --arrangements_files "barcode_arrs_nb12.cfg barcode_arrs_nb24.cfg"
+
+        for barcodes in fastq/barcode??; do
+            find -L \${barcodes} -name '*.fastq' -exec cat {} + | gzip > \${barcodes##*/}.fastq.gz
+        done
+
         cp fastq/*.txt fastq_tmp
         """
 }

nextflow.config

@@ -24,6 +24,7 @@ params {
     localguppy = false
     buildDB = false
     cloudProcess = false
+    one_end = false
 
     // parameters
     primerV = 'V3'

poreCov.nf

@@ -308,6 +308,8 @@ def helpMSG() {
     ${c_yellow}Parameters - Basecalling${c_reset}
     --localguppy    use a native guppy installation instead of a gpu-guppy-docker 
                     native guppy installation is used by default for singularity or conda
+    --one_end       removes the recommended "--require_barcodes_both_ends" from guppy demultiplexing
+                    try this if to many barcodes are unclassified (check the pycoQC report)
 
     ${c_yellow}Parameters - nCov genome reconstruction${c_reset}
     --primerV       artic-ncov2019 primer_schemes [default: ${params.primerV}]
@@ -363,20 +365,19 @@ def defaultMSG(){
        $params.output\u001B[0m
 
     Primerscheme: $params.primerV
+    Barcodes on one end enough?: $params.one_end
     CPUs to use: $params.cores
     Memory in GB: $params.memory
 
     \u001B[1;30m______________________________________\033[0m
     """.stripIndent()
 }
 
-
-
 def v1200_MSG() {
     log.info """
     1200 bp options are used as primer scheme (V1200)
-      --minLength set to 1000bp
-      --maxLength set to 1300bp
+      --minLength set to 250bp
+      --maxLength set to 1500bp
     \u001B[1;30m______________________________________\033[0m
     """.stripIndent()
 }