adapters trimming

00-scripts/step1.sf

@@ -19,14 +19,18 @@ rule process_radtags:
         enzyme=config["process_radtags"]["enzyme"],
         trim_length=config["process_radtags"]["trim_length"],
         score_limit=config["process_radtags"]["score_limit"],
+        windows_size=config["process_radtags"]["sliding_windows_size"],
+        adapter_mm=config["process_radtags"]["adapter_mm"],
         encoded=config["process_radtags"]["encoded"],
-        barcode_dist_1=config["process_radtags"]["barcode_dist_1"]
+        adapter_1=config["process_radtags"]["adapter_1"],
+        adapter_2=config["process_radtags"]["adapter_2"],
+        barcode_dist_1=config["process_radtags"]["barcode_dist_1"],
         barcode_dist_2=config["process_radtags"]["barcode_dist_2"]
     log:
         '10-logs/process_radtags/{runpool}.log'
     shell:
         '''mkdir -p {output};
-        process_radtags -i gzfastq -P -p {input} -o {output} -b 01-info_files/barcodes.txt -c -r -t {params.trim_length} --barcode_dist_1 {params.barcode_dist_1} --barcode_dist_2 {params.barcode_dist_2} -s {params.score_limit} -E {params.encoded} -e {params.enzyme} 2> {log}'''
+        process_radtags -i gzfastq -P -p {input} -o {output} -b 01-info_files/barcodes.txt -c -r -t {params.trim_length} --adapter_mm {params.adapter_mm} --adapter_1 {params.adapter_1} --adapter_2 {params.adapter_2} --barcode_dist_1 {params.barcode_dist_1} --barcode_dist_2 {params.barcode_dist_2} -w {params.windows_size} -s {params.score_limit} -E {params.encoded} -e {params.enzyme} 2> {log}'''
 
 ### clone filter
 rule clone_filter:

01-info_files/config.yaml

 process_radtags:
     enzyme : SbfI
-    trim_length : 143
+    trim_length : 142
     score_limit : 20
+    sliding_windows_size : 0.20
     encoded : phred33
-    barcode_dist_1 : 2
-    barcode_dist_2 : 2
+    barcode_dist_1 : 1
+    barcode_dist_2 : 1
+    adapter_mm : 2
+    adapter_1 : ACACTCTTTCCCTACACGACGCTCTTCCGATCT,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCAGAACAA,CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCC
+    adapter_2 : ACACTCTTTCCCTACACGACGCTCTTCCGATCT,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCAGAACAA,CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCC
 species:
  - mullus
  - serran

main.sh

@@ -11,7 +11,6 @@ if [[ -z $check_already_indexed ]]; then
     snakemake -s 00-scripts/step2.sf -j $CORES
 fi
 ## assign (run, pool, barcode) to individual according to _infos.csv file and align them onto the genome
-snakemake -s 00-scripts/step3.sf -j $CORES
+snakemake -s 00-scripts/step3.sf -j $CORES -F
 ## run STACKS2 programs : gstacks & populations
 snakemake -s 00-scripts/step4.sf -j $CORES
-