From 92a8ed7ec81eb15598c2fd0cff2cc74d38340c95 Mon Sep 17 00:00:00 2001
From: peguerin <pierre-edouard.guerin@cefe.cnrs.fr>
Date: Tue, 30 Oct 2018 14:06:27 +0100
Subject: [PATCH] adapters trimming
---
00-scripts/step1.sf | 8 ++++++--
01-info_files/config.yaml | 10 +++++++---
main.sh | 3 +--
3 files changed, 14 insertions(+), 7 deletions(-)
diff --git a/00-scripts/step1.sf b/00-scripts/step1.sf
index 580f2e4..43d27f8 100644
--- a/00-scripts/step1.sf
+++ b/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:
diff --git a/01-info_files/config.yaml b/01-info_files/config.yaml
index 3cba3df..539d00a 100644
--- a/01-info_files/config.yaml
+++ b/01-info_files/config.yaml
@@ -1,10 +1,14 @@
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
diff --git a/main.sh b/main.sh
index 4dd9cf2..24ec551 100644
--- a/main.sh
+++ b/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
-
--
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