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purge_dups.smk
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purge_dups.smk
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rule lr_mkref:
input:
fa = "results/fasta/{sample}_{version}.pseudohap.fasta.gz"
output:
directory("results/purge_dups/{sample}_{version}/refdata-{sample}_{version}.pseudohap"),
"results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.fa"
params:
tmp_fa = lambda w: f'results/purge_dups/{w.sample}_{w.version}/{w.sample}_{w.version}.pseudohap.fa'
log:
"logs/lr_mkref.{sample}_{version}.log",
container:
"containers/supernova.sif"
shell:
"""
zcat {input.fa} > {params.tmp_fa}
longranger mkref {params.tmp_fa} > {log} 2>&1
mv refdata-{wildcards.sample}_v1.pseudohap {output[0]}
"""
rule lr_align:
input:
expand("results/preprocessing/{{sample}}/{{sample}}_S1_L001_{R}_001.fastq.gz", R=["R1", "R2"]),
rules.lr_mkref.output
output:
directory("results/purge_dups/{sample}_{version}/lr_align_{sample}_{version}"),
"results/purge_dups/{sample}_{version}/lr_align_{sample}_{version}/outs/possorted_bam.bam"
params:
input_dir = lambda w, input: os.path.dirname(input[0]),
run_id = lambda w: f'{w.sample}_{w.version}',
sample = lambda w, input: re.sub("_S.+_L.+_R1_001.fastq.gz", "", os.path.basename(input[0])),
mem = config['supernova_mem']
threads:
workflow.cores
log:
"logs/lr_align.{sample}_{version}.log"
container:
"containers/supernova.sif"
shell:
"""
longranger align \
--id={params.run_id} \
--fastqs={params.input_dir} \
--sample={params.sample} \
--reference={input[2]} \
--localcores={threads} \
--localmem={params.mem} \
> {log} 2>&1
rm -r {output[0]} \
&& cp -al {params.run_id} {output[0]} \
&& rm -r {params.run_id}
"""
rule sort_by_name:
input:
"results/purge_dups/{sample}_{version}/lr_align_{sample}_{version}/outs/possorted_bam.bam"
output:
temp("results/purge_dups/{sample}_{version}/namesorted_bam.bam")
threads:
16
conda:
"../envs/mapping.yaml"
log:
"logs/purge_dups_samtools_namesort.{sample}_{version}.log"
threads:
config['purge_dups']['threads']
shell:
"samtools sort -@ {threads} -n -O BAM -o {output} {input} > {log} 2>&1"
rule ngscstat:
input:
"results/purge_dups/{sample}_{version}/namesorted_bam.bam"
output:
multiext("results/purge_dups/{sample}_{version}/TX", ".stat", ".base.cov")
params:
workdir = lambda w, output: os.path.dirname(output[0]),
input = "namesorted_bam.bam"
log:
"logs/purge_stats_ngscstat.{sample}_{version}.log"
shell:
"""
cd {params.workdir}
ngscstat {params.input} 2> ../../../{log}
"""
rule calcuts:
input:
multiext("results/purge_dups/{sample}_{version}/TX", ".stat", ".base.cov")
output:
"results/purge_dups/{sample}_{version}/cutoffs"
log:
"logs/purge_stats_calcuts.{sample}_{version}.log"
shell:
"""
calcuts {input[0]} > {output} 2> {log}
"""
rule make_hist:
input:
"results/purge_dups/{sample}/cutoffs",
"results/purge_dups/{sample}/TX.stat"
output:
"results/purge_dups/{sample}/hist_cutoffs.png"
shell:
"/opt/purge_dups/scripts/hist_plot.py "
"-c {input[0]} "
"{input[1]} "
"{output}"
rule split_fa_purge_dups:
input:
"results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.fa"
output:
temp("results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.split.fa")
log:
"logs/split_fa.{sample}_{version}.log"
shell:
"split_fa {input} > {output} 2> {log}"
rule self_map:
input:
"results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.split.fa"
output:
"results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.split.self.paf.gz"
log:
"logs/self_map.{sample}_{version}.log"
conda:
"../envs/mapping.yaml"
threads:
config['purge_dups']['threads']
shell:
"(minimap2 -t {threads} "
"-xasm5 -DP {input} {input} "
"| gzip -c - > {output}) 2> {log}"
rule purge_dups:
input:
selfmap = "results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.split.self.paf.gz",
basecov = "results/purge_dups/{sample}_{version}/TX.base.cov",
cutoffs = "results/purge_dups/{sample}_{version}/cutoffs"
output:
"results/purge_dups/{sample}_{version}/{sample}.dups.bed"
params:
M = config['purge_dups']['M'],
E = config['purge_dups']['E']
log:
"logs/purge_dups.{sample}_{version}.log"
shell:
"purge_dups -2 -M{params.M} -E{params.E} -T {input.cutoffs} "
"-c {input.basecov} {input.selfmap} > {output} "
"2> {log}"
rule get_sequences:
input:
bed = "results/purge_dups/{sample}_{version}/{sample}.dups.bed",
fa = "results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.fa",
hist = "results/purge_dups/{sample}_{version}/hist_cutoffs.png"
output:
purged = "results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.purged.fa.gz",
haps = "results/purge_dups/{sample}_{version}/{sample}_{version}.pseudohap.hap.fa.gz"
params:
prefix = lambda w, output: output[0].replace(".purged.fa.gz", "")
shell:
"""
get_seqs {input.bed} {input.fa} \
-p {params.prefix}
gzip {params.prefix}.*.fa
"""
rule copy_output_v3:
input:
"results/purge_dups/{sample}_v2/{sample}_v2.pseudohap.purged.fa.gz"
output:
protected("results/fasta/{sample}_v3.pseudohap.fasta.gz")
shell:
"cp {input} {output}"
rule copy_output_v4:
input:
"results/purge_dups/{sample}_v1/{sample}_v1.pseudohap.purged.fa.gz"
output:
protected("results/fasta/{sample}_v4.pseudohap.fasta.gz")
shell:
"cp {input} {output}"