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[MISC] Clean up parameters in Snakemake workflow
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Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
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@Irallia
Irallia committed Sep 17, 2021
1 parent 766b72d commit 7c72242
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Showing 3 changed files with 46 additions and 59 deletions.
21 changes: 6 additions & 15 deletions test/benchmark/caller_comparison/config/config.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
long_bam: data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio_sorted.bam
long_bam_md: data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio_sorted.md.bam
long_md_bam: data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio_sorted.md.bam
long_bai: data/long_reads/HG002.Sequel.10kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio_sorted.bam.bai

reference_fa_gz: data/reference/hs37d5.fa.gz
Expand All @@ -9,18 +9,9 @@ parameters:
sample: HG002
min_var_length: 40
max_var_length: 1000000
min_qual: 2

minimums:
igenvar_from: 1
igenvar_to: 80
igenvar_step: 2
svim_from: 1
svim_to: 80
svim_step: 2
sniffles_from: 1
sniffles_to: 80
sniffles_step: 2
pbsv_from: 1
pbsv_to: 80
pbsv_step: 2
quality_ranges:
igenvar: {from: 1, to: 80, step: 2}
svim: {from: 1, to: 80, step: 2}
sniffles: {from: 1, to: 80, step: 2}
pbsv: {from: 1, to: 80, step: 2}
60 changes: 28 additions & 32 deletions test/benchmark/caller_comparison/workflow/rules/callers.smk
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Original file line number Diff line number Diff line change
@@ -1,22 +1,24 @@
wildcard_constraints:
sample = config["parameters"]["sample"],
min_var_length = config["parameters"]["min_var_length"],
max_var_length = config["parameters"]["max_var_length"]

rule run_igenvar:
input:
bam = config["long_bam"]
output:
vcf = "results/caller_comparison/iGenVar/variants.vcf"
params:
sample = config["parameters"]["sample"],
min_qual = config["parameters"]["min_qual"],
min_var_length = config["parameters"]["min_var_length"],
max_var_length = config["parameters"]["max_var_length"]
min_qual = config["parameters"]["min_qual"]
shell:
"""
./build/iGenVar/bin/iGenVar -t 1 -j {input.bam} -o {output.vcf} \
--vcf_sample_name {params.sample} \
--vcf_sample_name {sample} \
--method cigar_string \
--method split_read \
--min_var_length {params.min_var_length} \
--max_var_length {params.max_var_length} \
--min_qual {params.min_qual}
--min_var_length {min_var_length} \
--max_var_length {max_var_length} \
--min_qual 2
"""
# Defaults:
# --clustering_methods hierarchical_clustering --refinement_methods no_refinement
Expand All @@ -36,24 +38,21 @@ rule run_svim:
io_gb = 100
params:
working_dir = "results/caller_comparison/SVIM/",
sample = config["parameters"]["sample"],
min_var_length = config["parameters"]["min_var_length"],
max_var_length = config["parameters"]["max_var_length"]
threads: 1
conda:
"../../../envs/svim.yaml"
shell:
"""
svim alignment --sample {params.sample} \
svim alignment --sample {sample} \
--partition_max_distance 1000 \
--cluster_max_distance 0.5 \
--min_sv_size {params.min_var_length} \
--min_sv_size {min_var_length} \
--segment_gap_tolerance 20 \
--segment_overlap_tolerance 20 \
--interspersed_duplications_as_insertions \
--tandem_duplications_as_insertions \
--read_names \
--max_sv_size {params.max_var_length} \
--max_sv_size {max_var_length} \
--verbose \
{params.working_dir} {input.bam} {input.genome}
"""
Expand All @@ -63,22 +62,20 @@ rule run_svim:
# SNIFFLES (we have to loop over min_support, because sniffles does not write a quality score into the vcf)
rule run_sniffles:
input:
bam = config["long_bam_md"],
bam = config["long_md_bam"],
output:
expand("results/caller_comparison/Sniffles/raw_variants.{minsupport}.vcf",
minsupport=list(range(config["minimums"]["sniffles_from"],
config["minimums"]["sniffles_to"]+1,
config["minimums"]["sniffles_step"])))
minsupport=list(range(config["quality_ranges"]["sniffles"]["from"],
config["quality_ranges"]["sniffles"]["to"]+1,
config["quality_ranges"]["sniffles"]["step"])))
resources:
mem_mb = 400000,
time_min = 1200,
io_gb = 100
params:
min_support = config["parameters"]["min_qual"],
min_length = config["parameters"]["min_var_length"],
qual_from = config["minimums"]["sniffles_from"],
qual_to = config["minimums"]["sniffles_to"]+1,
qual_step = config["minimums"]["sniffles_step"]
qual_from = config["quality_ranges"]["sniffles"]["from"],
qual_to = config["quality_ranges"]["sniffles"]["to"]+1,
qual_step = config["quality_ranges"]["sniffles"]["step"]
threads: 10
conda:
"../../../envs/sniffles.yaml"
Expand All @@ -87,7 +84,7 @@ rule run_sniffles:
for i in $(seq {params.qual_from} {params.qual_step} {params.qual_to})
do
sniffles --mapped_reads {input.bam} --vcf results/caller_comparison/Sniffles/raw_variants.$i.vcf \
--min_support $i --min_length {params.min_length} --threads {threads} --genotype
--min_support $i --min_length {min_var_length} --threads {threads} --genotype
done
"""

Expand Down Expand Up @@ -137,18 +134,17 @@ rule run_pbsv_call:
svsig_gz = dynamic("results/caller_comparison/pbsv/signatures.{region}.svsig.gz")
output:
vcf = expand("results/caller_comparison/pbsv/variants.min_qual_{minsupport}.vcf",
minsupport=list(range(config["minimums"]["pbsv_from"],
config["minimums"]["pbsv_to"]+1,
config["minimums"]["pbsv_step"])))
minsupport=list(range(config["quality_ranges"]["pbsv"]["from"],
config["quality_ranges"]["pbsv"]["to"]+1,
config["quality_ranges"]["pbsv"]["step"])))
resources:
mem_mb = 400000,
time_min = 2000,
io_gb = 100
params:
min_sv_length = config["parameters"]["min_var_length"],
qual_from = config["minimums"]["pbsv_from"],
qual_to = config["minimums"]["pbsv_to"]+1,
qual_step = config["minimums"]["pbsv_step"]
qual_from = config["quality_ranges"]["pbsv"]["from"],
qual_to = config["quality_ranges"]["pbsv"]["to"]+1,
qual_step = config["quality_ranges"]["pbsv"]["step"]
threads: 1
conda:
"../../../envs/pbsv.yaml"
Expand All @@ -157,7 +153,7 @@ rule run_pbsv_call:
"""
for i in $(seq {params.qual_from} {params.qual_step} {params.qual_to})
do
pbsv call --types DEL,INS --min-sv-length {params.min_sv_length} --max-ins-length 100K \
pbsv call --types DEL,INS --min-sv-length {min_var_length} --max-ins-length 100K \
--call-min-reads-all-samples $i --call-min-reads-one-sample $i \
--call-min-reads-per-strand-all-samples 0 --call-min-bnd-reads-all-samples 0 --call-min-read-perc-one-sample 0 \
--num-threads {threads} {input.genome} {input.svsig_gz} results/caller_comparison/pbsv/variants.min_qual_$i.vcf
Expand Down
24 changes: 12 additions & 12 deletions test/benchmark/caller_comparison/workflow/rules/eval.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -53,21 +53,21 @@ rule reformat_truvari_results:
rule cat_truvari_results_all:
input:
igenvar = expand("results/caller_comparison/eval/iGenVar/min_qual_{min_qual}/pr_rec.txt",
min_qual=list(range(config["minimums"]["igenvar_from"],
config["minimums"]["igenvar_to"]+1,
config["minimums"]["igenvar_step"]))),
min_qual=list(range(config["quality_ranges"]["igenvar"]["from"],
config["quality_ranges"]["igenvar"]["to"]+1,
config["quality_ranges"]["igenvar"]["step"]))),
svim = expand("results/caller_comparison/eval/SVIM/min_qual_{min_qual}/pr_rec.txt",
min_qual=list(range(config["minimums"]["svim_from"],
config["minimums"]["svim_to"]+1,
config["minimums"]["svim_step"]))),
min_qual=list(range(config["quality_ranges"]["svim"]["from"],
config["quality_ranges"]["svim"]["to"]+1,
config["quality_ranges"]["svim"]["step"]))),
sniffles = expand("results/caller_comparison/eval/Sniffles/min_qual_{min_qual}/pr_rec.txt",
min_qual=list(range(config["minimums"]["sniffles_from"],
config["minimums"]["sniffles_to"]+1,
config["minimums"]["sniffles_step"]))),
min_qual=list(range(config["quality_ranges"]["sniffles"]["from"],
config["quality_ranges"]["sniffles"]["to"]+1,
config["quality_ranges"]["sniffles"]["step"]))),
pbsv = expand("results/caller_comparison/eval/pbsv/min_qual_{min_qual}/pr_rec.txt",
min_qual=list(range(config["minimums"]["pbsv_from"],
config["minimums"]["pbsv_to"]+1,
config["minimums"]["pbsv_step"])))
min_qual=list(range(config["quality_ranges"]["pbsv"]["from"],
config["quality_ranges"]["pbsv"]["to"]+1,
config["quality_ranges"]["pbsv"]["step"])))
output:
igenvar = temp("results/caller_comparison/eval/igenvar.all_results.txt"),
svim = temp("results/caller_comparison/eval/svim.all_results.txt"),
Expand Down

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