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add resources/mem_mb and more temp() in rules
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@pmenzel
pmenzel committed Jan 24, 2024
1 parent 1cfae08 commit bac81b2
Showing 1 changed file with 46 additions and 12 deletions.
58 changes: 46 additions & 12 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ if config.get("run_score_assemblies", False):

module score_assemblies:
snakefile:
github("pmenzel/score-assemblies", path="Snakefile", branch="master")
# "score-assemblies/Snakefile"
github("pmenzel/score-assemblies", path="Snakefile", branch="master")
config:
config

Expand Down Expand Up @@ -273,21 +273,25 @@ rule filtlongMBqln:
rule miniasm:
conda:
"env/conda-miniasm.yaml"
threads: 10
threads: 5
resources:
mem_mb=12000,
input:
fqont=get_ont_fq,
output:
fa="assemblies/{sample}_miniasm/output.fa",
paf=temp("assemblies/{sample}_miniasm/minimap2_overlap.paf"),
gfa="assemblies/{sample}_miniasm/minimap2_miniasm.gfa",
link="assemblies/{sample}_miniasm.fa",
log:
"assemblies/{sample}_miniasm/log.txt",
benchmark:
"benchmark/{sample}_miniasm.txt"
shell:
"""
minimap2 -x ava-ont -t {threads} {input} {input} > assemblies/{wildcards.sample}_miniasm/minimap2_overlap.paf 2>{log}
miniasm -f {input} assemblies/{wildcards.sample}_miniasm/minimap2_overlap.paf > assemblies/{wildcards.sample}_miniasm/minimap2_miniasm.gfa 2>>{log}
perl -lsane 'print ">$F[1]\n$F[2]" if $F[0] =~ /S/;' assemblies/{wildcards.sample}_miniasm/minimap2_miniasm.gfa > {output.fa} 2>>{log}
minimap2 -x ava-ont -t {threads} {input} {input} > {output.paf} 2>{log}
miniasm -f {input} {output.paf} > {output..gfa} 2>>{log}
perl -lsane 'print ">$F[1]\n$F[2]" if $F[0] =~ /S/;' {output.gfa} > {output.fa} 2>>{log}
ln -sr {output.fa} {output.link}
"""

Expand All @@ -296,6 +300,8 @@ rule unicycler:
conda:
"env/conda-unicycler.yaml"
threads: 10
resources:
mem_mb=12000,
input:
fqont=get_ont_fq,
fq1=get_R1_fq,
Expand All @@ -322,6 +328,8 @@ rule flye:
conda:
"env/conda-flye.yaml"
threads: 5
resources:
mem_mb=12000,
input:
fq=get_ont_fq,
output:
Expand All @@ -343,6 +351,8 @@ rule flyeX:
conda:
"env/conda-flye.yaml"
threads: 5
resources:
mem_mb=12000,
input:
fq=get_ont_fq,
output:
Expand All @@ -365,6 +375,8 @@ rule flyehq:
conda:
"env/conda-flye.yaml"
threads: 5
resources:
mem_mb=12000,
input:
fq=get_ont_fq,
output:
Expand All @@ -386,6 +398,8 @@ rule flyehqX:
conda:
"env/conda-flye.yaml"
threads: 5
resources:
mem_mb=12000,
input:
fq=get_ont_fq,
output:
Expand All @@ -408,6 +422,8 @@ rule raven:
conda:
"env/conda-raven.yaml"
threads: 5
resources:
mem_mb=5000,
input:
fq=get_ont_fq,
output:
Expand All @@ -429,6 +445,8 @@ rule ravenX:
conda:
"env/conda-raven.yaml"
threads: 5
resources:
mem_mb=5000,
input:
fq=get_ont_fq,
output:
Expand All @@ -448,7 +466,9 @@ rule ravenX:
rule canu:
conda:
"env/conda-canu.yaml"
threads: 10
threads: 5
resources:
mem_mb=12000,
input:
fqont=get_ont_fq,
output:
Expand Down Expand Up @@ -543,6 +563,8 @@ rule medaka:
conda:
"env/conda-medaka.yaml"
threads: 5
resources:
mem_mb=12000,
input:
prev_fa="assemblies/{sample}_{assembly}/output.fa",
fq=get_ont_fq,
Expand All @@ -567,12 +589,14 @@ rule pilon:
conda:
"env/conda-pilon.yaml"
threads: 5
resources:
mem_mb=12000,
input:
prev_fa="assemblies/{sample}_{assembly}/output.fa",
fq1=get_R1_fq,
fq2=get_R2_fq,
output:
bam="assemblies/{sample}_{assembly}+pilon/map.bam",
bam=temp("assemblies/{sample}_{assembly}+pilon/map.bam"),
fa="assemblies/{sample}_{assembly}+pilon/output.fa",
link="assemblies/{sample}_{assembly}+pilon.fa",
log:
Expand All @@ -584,7 +608,7 @@ rule pilon:
bwa index -p assemblies/{wildcards.sample}_{wildcards.assembly}+pilon/bwa_index {input.prev_fa} >{log} 2>&1
bwa mem -t {threads} assemblies/{wildcards.sample}_{wildcards.assembly}+pilon/bwa_index {input.fq1} {input.fq2} 2>>{log} | samtools sort -o {output.bam} - 2>>{log}
samtools index {output.bam} 2>>{log}
pilon -Xmx60G --genome {input.prev_fa} --frags {output.bam} --outdir assemblies/{wildcards.sample}_{wildcards.assembly}+pilon/ --output pilon --changes --vcf >>{log} 2>&1
pilon -Xmx60G --genome {input.prev_fa} --frags {output.bam} --outdir assemblies/{wildcards.sample}_{wildcards.assembly}+pilon/ --output pilon --changes >>{log} 2>&1
mv assemblies/{wildcards.sample}_{wildcards.assembly}+pilon/pilon.fasta {output.fa}
ln -sr {output.fa} {output.link}
"""
Expand All @@ -594,6 +618,8 @@ rule polca:
conda:
"env/conda-masurca.yaml"
threads: 5
resources:
mem_mb=5000,
shadow:
"minimal"
input:
Expand All @@ -619,11 +645,17 @@ rule polypolish:
conda:
"env/conda-polypolish.yaml"
threads: 5
resources:
mem_mb=4000,
input:
prev_fa="assemblies/{sample}_{assembly}/output.fa",
fq1=get_R1_fq,
fq2=get_R2_fq,
output:
samR1=temp("assemblies/{sample}_{assembly}+polypolish/alignments_R1.sam"),
samR2=temp("assemblies/{sample}_{assembly}+polypolish/alignments_R2.sam"),
filtered_samR1=temp("assemblies/{sample}_{assembly}+polypolish/filtered_R1.sam"),
filtered_samR2=temp("assemblies/{sample}_{assembly}+polypolish/filtered_R2.sam"),
fa="assemblies/{sample}_{assembly}+polypolish/output.fa",
link="assemblies/{sample}_{assembly}+polypolish.fa",
log:
Expand All @@ -633,10 +665,10 @@ rule polypolish:
shell:
"""
bwa index -p assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/bwa_index {input.prev_fa} >{log} 2>&1
bwa mem -a -t {threads} assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/bwa_index {input.fq1} > assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/alignments_R1.sam 2>>{log}
bwa mem -a -t {threads} assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/bwa_index {input.fq2} > assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/alignments_R2.sam 2>>{log}
polypolish_insert_filter.py --in1 assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/alignments_R1.sam --in2 assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/alignments_R2.sam --out1 assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/filtered_R1.sam --out2 assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/filtered_R2.sam >>{log} 2>&1
polypolish {input.prev_fa} assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/filtered_R1.sam assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/filtered_R2.sam > {output.fa} 2>>{log}
bwa mem -a -t {threads} assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/bwa_index {input.fq1} > {output.samR1} 2>>{log}
bwa mem -a -t {threads} assemblies/{wildcards.sample}_{wildcards.assembly}+polypolish/bwa_index {input.fq2} > {output.samR2} 2>>{log}
polypolish_insert_filter.py --in1 {output.samR1} --in2 {output.samR2} --out1 {output.filtered_samR1} --out2 {output.filtered_samR2} >>{log} 2>&1
polypolish {input.prev_fa} {output.filtered_samR1} {output.filtered_samR2} > {output.fa} 2>>{log}
ln -sr {output.fa} {output.link}
"""

Expand Down Expand Up @@ -687,6 +719,8 @@ rule proovframe:
conda:
"env/conda-proovframe.yaml"
threads: 1
resources:
mem_mb=4000,
input:
prev_fa="assemblies/{sample}_{assembly}/output.fa",
ref="references-protein/{ref}.dmnd",
Expand Down

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