From bf2e910a77240d480a1fc3c4c8deb2cae026dfa7 Mon Sep 17 00:00:00 2001 From: alienzj Date: Fri, 19 Aug 2022 15:01:12 +0800 Subject: [PATCH] support fastp --dedup --- metapi/config/config.yaml | 2 ++ metapi/rules/trimming.smk | 8 +++++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/metapi/config/config.yaml b/metapi/config/config.yaml index a5654079..50f23a2e 100644 --- a/metapi/config/config.yaml +++ b/metapi/config/config.yaml @@ -45,6 +45,8 @@ params: cut_right_mean_quality: 20 length_required: 51 n_base_limit: 5 + dedup: False + dup_calc_accuracy: 3 # [1, 2, 3, 4, 5, 6] # only used when dedup: True rmhost: host_fasta: "/home/jiezhu/databases/genomics/human/CHM13/chm13v2.0_plusY/chm13v2.0.fa" diff --git a/metapi/rules/trimming.smk b/metapi/rules/trimming.smk index 80f96003..3571f0e0 100644 --- a/metapi/rules/trimming.smk +++ b/metapi/rules/trimming.smk @@ -118,7 +118,9 @@ if config["params"]["trimming"]["fastp"]["do"]: length_required = config["params"]["trimming"]["fastp"]["length_required"], n_base_limit = config["params"]["trimming"]["fastp"]["n_base_limit"], use_slide_window = "yes" if config["params"]["trimming"]["fastp"]["use_slide_window"] else "no", - pe = "pe" if IS_PE else "se" + pe = "pe" if IS_PE else "se", + dedup = f'''--dedup --dup_calc_accuracy {config["params"]["trimming"]["fastp"]["dup_calc_accuracy"]}''' \ + if config["params"]["trimming"]["fastp"]["dedup"] else "" log: os.path.join(config["output"]["trimming"], "logs/{sample}.fastp.log") benchmark: @@ -141,6 +143,7 @@ if config["params"]["trimming"]["fastp"]["do"]: --out2 {output.reads[1]} \ --compression {params.compression} \ {ADAPTER_OPERATION} \ + {params.dedup} \ --cut_front \ --cut_right \ --cut_front_window_size {params.cut_front_window_size} \ @@ -160,6 +163,7 @@ if config["params"]["trimming"]["fastp"]["do"]: --out2 {output.reads[1]} \ --compression {params.compression} \ {ADAPTER_OPERATION} \ + {params.dedup} \ --cut_front \ --cut_tail \ --cut_front_window_size {params.cut_front_window_size} \ @@ -180,6 +184,7 @@ if config["params"]["trimming"]["fastp"]["do"]: --out1 {output.reads[0]} \ --compression {params.compression} \ {ADAPTER_OPERATION} \ + {params.dedup} \ --cut_front \ --cut_right \ --cut_front_window_size {params.cut_front_window_size} \ @@ -197,6 +202,7 @@ if config["params"]["trimming"]["fastp"]["do"]: --out1 {output.reads[0]} \ --compression {params.compression} \ {ADAPTER_OPERATION} \ + {params.dedup} \ --cut_front \ --cut_tail \ --cut_front_window_size {params.cut_front_window_size} \