From 776827fba3f80a3127d5d10cd21786b4856b560e Mon Sep 17 00:00:00 2001
From: papanikos <n.pappas@uu.nl>
Date: Thu, 14 Jan 2021 21:05:52 +0100
Subject: [PATCH] add size filtering rule
---
workflow/Snakefile | 30 ++++++++++++++++++++----------
1 file changed, 20 insertions(+), 10 deletions(-)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 415e26c..ff19b64 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -51,6 +51,7 @@ def collect_prediction_tsvs(wc):
rule all:
input:
expand([
+ "results/{sample}/tmp/filtered.fa.gz",
"results/{sample}/tmp/reflist.txt",
"results/{sample}/{tool}/predictions.tsv",
"results/{sample}/all_predictions.tsv",
@@ -61,9 +62,24 @@ rule all:
###########
## RULES ##
###########
-rule split_multifasta:
+
+rule size_filter:
input:
multifasta_fp = get_sample_fasta
+ output:
+ filtered_fasta = "results/{sample}/tmp/filtered.fa.gz"
+ threads: 4
+ log:
+ "logs/{sample}/size_filter.log"
+ params:
+ min_size = 5000
+ shell:
+ "seqkit seq -g -j {threads} -m {params.min_size} "
+ "{input.multifasta_fp} | gzip -c >{output.filtered_fasta} 2>{log}"
+
+rule split_multifasta:
+ input:
+ multifasta_fp = rules.size_filter.output.filtered_fasta
output:
reflist = "results/{sample}/tmp/reflist.txt"
log: "logs/{sample}/split_multifasta.log"
@@ -109,8 +125,6 @@ rule filter_vhulk:
# RAFAH
rule run_rafah:
input:
- # Run vhulk first since it writing in the input
- rules.run_vhulk.output.done_txt,
reflist = rules.split_multifasta.output.reflist,
output:
seq_info = "results/{sample}/rafah/{sample}_Seq_Info.tsv"
@@ -140,8 +154,6 @@ rule filter_rafah:
# VirHostMatcher-Net
rule run_vhmnet:
input:
- # Run vhulk first since it writing in the input
- rules.run_vhulk.output.done_txt,
reflist = rules.split_multifasta.output.reflist,
output:
done = touch("results/{sample}/vhmnet/.done.txt")
@@ -149,11 +161,10 @@ rule run_vhmnet:
# use it with
# snakemake --singularity-args "-B /path/to/data/:/data" ...
data_dir = "/data",
- #data_dir = DATA_DIR,
tmp_dir = "results/{sample}/vhmnet/tmp",
output_dir = "results/{sample}/vhmnet",
fasta_dir = "results/{sample}/tmp/genomes"
- threads: 8
+ threads: 12
container:
"library://papanikos_182/default/vhmnet:0.1"
log:
@@ -204,7 +215,6 @@ rule run_wish:
# snakemake --singularity-args binds the whole data dir to /data
# see run_vhmnet rule
models_dir = "/data/host_wish_model",
- #models_dir = DATA_DIR.joinpath("host_wish_model"),
output_dir = "results/{sample}/wish",
fasta_dir = "results/{sample}/tmp/genomes"
shell:
@@ -247,7 +257,7 @@ rule run_htp:
pred=$(viruses_classifier \
--classifier svc \
--nucleic_acid dna \
- -p ${{f}}) 2>{log.stderr}
+ -p ${{f}} 2>{log.stderr})
echo -e $contig_id\t$pred >> {output.htp_raw}
done
"""
@@ -261,7 +271,7 @@ rule process_htp:
ob = "{"
shell:
"""
- tail -n +2 results/A/htp/raw.txt | cut -f1 -d','| \
+ tail -n +2 results/{wildcards.sample}/htp/raw.txt | cut -f1 -d','| \
sed -r "s/ \{params.ob}'phage'\: /\t/" | sort -k1 \
>{output.predictions_tsv}
"""
--
GitLab