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Commit bd5ee96d authored by james94's avatar james94
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slurm optimisation

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SUBMIT_CONFIG/slurm/cluster.yaml 0 → 100644
+ 105
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View file @ bd5ee96d
__default__:
jobname: 'GEP.{rule}'
partition: begendiv
nCPUs: "{threads}"
qos: 'standard'
nodes: 1
unzipFasta_PRI:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
symlinkUnzippedFasta_PRI:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
unzipFasta_ALT:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
symlinkUnzippedFasta_ALT:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
busco5:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 100000
time: "1-00:00:00"
moveBuscoOutputs:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
merqury:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 20000
time: "08:00:00"
genomescope2:
jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
memory: 500
time: "00:00:05"
assemblyStats:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
saveConfiguration_and_getKeyValues_kmer:
jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
memory: 500
time: "00:00:05"
saveConfiguration_and_getKeyValues:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:00:05"
aggregateAllAssemblies:
jobname: GEP.{rule}
memory: 500
time: "00:00:05"
makeReport:
jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
memory: 500
time: "00:00:05"
addFullTable:
jobname: GEP.{rule}
memory: 500
time: "00:00:05"
aggregateReport:
jobname: GEP.{rule}
memory: 500
time: "00:00:05"
makePDF:
jobname: GEP.{rule}
memory: 500
time: "00:00:05"
SUBMIT_CONFIG/slurm/config.yaml
+ 20
− 16
View file @ bd5ee96d
cluster-config: "cluster.yaml"
cluster: cluster:
mkdir -p logs/{rule} && mkdir -p slurm_logs/{rule} &&
sbatch sbatch
--partition={resources.partition} --partition={cluster.partition}
--qos={resources.qos} --qos={cluster.qos}
--cpus-per-task={threads} --cpus-per-task={cluster.nCPUs}
--mem={resources.mem_mb} --mem={cluster.memory}
--job-name=smk-{rule}-{wildcards} --job-name={cluster.jobname}
--output=logs/{rule}/{rule}-{wildcards}-%j.out --output=slurm_logs/{rule}/{rule}-{wildcards}-%j.out
--time={resources.time} --time={cluster.time}
--nodes={resources.nodes} --nodes={cluster.nodes}
#User Defines below parameters #User Defines below parameters
default-resources: # default-resources:
- partition=begendiv # - partition=begendiv
- qos=standard # - qos=standard
- mem_mb=100000 # - mem_mb=100000
- time="3-00:00:00" # - time="3-00:00:00"
- nodes=1 # - nodes=1
restart-times: 3 restart-times: 3
max-jobs-per-second: 100 max-jobs-per-second: 100
max-status-checks-per-second: 10 max-status-checks-per-second: 10
local-cores: 1
latency-wait: 60 latency-wait: 60
jobs: 500 jobs: 500
keep-going: False keep-going: False
......
configuration/exampleSampleSheets/build_hifi_example.tsv
+ 3
− 6
View file @ bd5ee96d
sample hifi_reads meryl_kmer_size trimSMRTbell fastQC sample hifi_reads meryl_kmer_size trimSMRTbell fastQC
ilLasFlex1.1 /srv/public/users/james94/data/ilLasFlex1.1/ERR6565937.fastq 21 True True organismX /<pathto>/organismX_Hifi_Library1.fq 21 False True
ilVanAtal1.2 /srv/public/users/james94/data/ilVanAtal1.2/ERR6608650.fastq 21 False True organismX /<pathto>/organismX_Hifi_Library2.fq 21 False True
ilCyaSemi1.1 /srv/public/users/james94/data/ilCyaSemi1.1/ERR6560795.fastq 21 False True
idScaPyra1.1 /srv/public/users/james94/data/idScaPyra1.1/ERR7057609.fastq 21 True True
idScaPyra1.1 /srv/public/users/james94/data/idScaPyra1.1/ERR7057610.fastq 21 True True
configuration/exampleSampleSheets/build_illumina_example.tsv
+ 6
− 7
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sample Library_R1 Library_R2 meryl_kmer_size trim10X trimAdapters fastQC sample Library_R1 Library_R2 meryl_kmer_size trim10X trimAdapters fastQC
ilVanAtal1.2 /srv/public/users/james94/data/ilVanAtal1.2/30996_8_1_R1.trimmed.fq /srv/public/users/james94/data/ilVanAtal1.2/30996_8_1_R2.trimmed.fq 21 False False True organismX /<pathto>/organismX_Library1_R1.fq /<pathto>/organismX_Library1_R2.fq 21 False False True
ilVanAtal1.2 /srv/public/users/james94/data/ilVanAtal1.2/30996_8_3_R1.trimmed.fq /srv/public/users/james94/data/ilVanAtal1.2/30996_8_3_R2.trimmed.fq 21 False False True organismX /<pathto>/organismX_Library2_R1.fq /<pathto>/organismX_Library2_R2.fq 21 False False True
ilLasFlex1.1 /srv/public/users/james94/data/ilLasFlex1.1/ERR6002656_1.fastq.gz /srv/public/users/james94/data/ilLasFlex1.1/ERR6002656_2.fastq.gz 21 True True True organismY /<pathto>/organismY_Library1_R1.fastq.gz /<pathto>/organismY_Library1_R2.fastq.gz 21 True True True
ilLasFlex1.1 /srv/public/users/james94/data/ilLasFlex1.1/ERR6003042_1.fastq /srv/public/users/james94/data/ilLasFlex1.1/ERR6003042_2.fastq 21 True True True organismY /<pathto>/organismY_Library2_R1.fastq.gz /<pathto>/organismY_Library2_R2.fastq.gz 21 True True True
ilCyaSemi1.1 /srv/public/users/james94/data/ilCyaSemi1.1/ERR6002620_1.fastq.gz /srv/public/users/james94/data/ilCyaSemi1.1/ERR6002620_2.fastq.gz 21 True True True organismY /<pathto>/organismY_Library3_R1.fastq.gz /<pathto>/organismY_Library3_R2.fastq.gz 21 True True True
ilCyaSemi1.1 /srv/public/users/james94/data/ilCyaSemi1.1/ERR6002621_1.fastq.gz /srv/public/users/james94/data/ilCyaSemi1.1/ERR6002621_2.fastq.gz 21 True True True
configuration/exampleSampleSheets/runEval_example.tsv
+ 4
− 4
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ID PRI_asm ALT_asm merylDB merylDB_kmer genomeSize ID PRI_asm ALT_asm merylDB merylDB_kmer genomeSize
ilVanAtal1.2_HifiDB /srv/public/users/james94/ilVanAtal1.2/GCA_905147765.2_ilVanAtal1.2_genomic.fna.gz None /srv/public/users/james94/ilVanAtal1.2/complete_hifi_ilVanAtal1.2_dB.smrtTrimmed.21.meryl 21 speciesX_illumina /<pathto>/speciesX_assembly.fasta None /<pathTo>/speciesX_illumina_database.21.meryl 21
ilLasFlex1.1_IllumDB /srv/public/users/james94/ilLasFlex1.1/GCA_905147015.1_ilLasFlex1.1_genomic.fna None /srv/public/users/james94/ilLasFlex1.1/complete_Illumina_ilLasFlex1.1_dB.10xTrimmed.AdaptTrimmed.21.meryl 21 speciesX_HiFi /<pathto>/speciesX_assembly.fasta None /<pathTo>/speciesX_hifi_database.31.meryl 31
ilCyaSemi1.1_HifiDB /srv/public/users/james94/ilCyaSemi1.1/GCA_905187585.1_ilCyaSemi1.1_genomic.fna.gz None /srv/public/users/james94/ilCyaSemi1.1/complete_hifi_ilCyaSemi1.1_dB.smrtTrimmed.21.meryl 21 speciesY_illumina /<pathto>/speciesY_assembly_PrimaryHaplotype.fasta /<pathto>/speciesY_assembly_AlternateHaplotype.fasta /<pathTo>/speciesy_illumina_database.21.meryl 21 1050000
rules/run_05_11_21.smk
+ 31
− 3
View file @ bd5ee96d
...@@ -38,6 +38,8 @@ rule unzipFasta_PRI: ...@@ -38,6 +38,8 @@ rule unzipFasta_PRI:
os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.PRI.pigzUnzip.log") os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.PRI.pigzUnzip.log")
conda: conda:
"../envs/pigz.yaml" "../envs/pigz.yaml"
threads:
1
shell: shell:
""" """
pigz -c -d -k {input.assembly} > {output} 2> {log} pigz -c -d -k {input.assembly} > {output} 2> {log}
...@@ -48,6 +50,8 @@ rule symlinkUnzippedFasta_PRI: ...@@ -48,6 +50,8 @@ rule symlinkUnzippedFasta_PRI:
assembly=PRI_asm_unzipped, assembly=PRI_asm_unzipped,
output: output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.PRI.fasta")), temp(os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.PRI.fasta")),
threads:
1
shell: shell:
""" """
ln -s {input} {output} ln -s {input} {output}
...@@ -62,6 +66,8 @@ rule unzipFasta_ALT: ...@@ -62,6 +66,8 @@ rule unzipFasta_ALT:
os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.ALT.pigzUnzip.log") os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.ALT.pigzUnzip.log")
conda: conda:
"../envs/pigz.yaml" "../envs/pigz.yaml"
threads:
1
shell: shell:
""" """
pigz -c -d -k {input.assembly} > {output} 2> {log} pigz -c -d -k {input.assembly} > {output} 2> {log}
...@@ -72,6 +78,8 @@ rule symlinkUnzippedFasta_ALT: ...@@ -72,6 +78,8 @@ rule symlinkUnzippedFasta_ALT:
assembly=ALT_asm_unzipped, assembly=ALT_asm_unzipped,
output: output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.ALT.fasta")), temp(os.path.join(config['Results'], "1_evaluation/{asmID}/01_unzipFastas/{asmID}.ALT.fasta")),
threads:
1
shell: shell:
""" """
ln -s {input} {output} ln -s {input} {output}
...@@ -87,7 +95,7 @@ rule busco5: ...@@ -87,7 +95,7 @@ rule busco5:
assemblyName = "{asmID}", assemblyName = "{asmID}",
chngDir = os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO") chngDir = os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO")
threads: threads:
workflow.cores * 0.25 16
output: output:
# report(os.path.join(config['Results'], "{sample}" + "/busco5/" + "{sample}" + "/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt"), caption="../report/busco.rst", category="Benchmark Universal Single Copy Orthologs", subcategory="{fastq}") # report(os.path.join(config['Results'], "{sample}" + "/busco5/" + "{sample}" + "/short_summary.specific." + config['busco5Lineage'] + "_odb10." + "{sample}" + ".txt"), caption="../report/busco.rst", category="Benchmark Universal Single Copy Orthologs", subcategory="{fastq}")
os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO/{asmID}/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"), os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO/{asmID}/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"),
...@@ -123,6 +131,8 @@ rule moveBuscoOutputs: ...@@ -123,6 +131,8 @@ rule moveBuscoOutputs:
# blastDB= os.path.join(config['Results'], "{sample}" + "/busco5/blast_db") # blastDB= os.path.join(config['Results'], "{sample}" + "/busco5/blast_db")
output: output:
file = os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"), file = os.path.join(config['Results'], "1_evaluation/{asmID}/05_BUSCO/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"),
threads:
1
shell: shell:
""" """
mv -t {params.mvRunBuscoDest} {params.logs} mv -t {params.mvRunBuscoDest} {params.logs}
...@@ -149,7 +159,7 @@ rule merqury: ...@@ -149,7 +159,7 @@ rule merqury:
# symlink_fasta=os.path.join(config['Results'], "01_evaluation/{asmID}/01B_QV-and-kmerMultiplicity/{asmID}.fasta"), # symlink_fasta=os.path.join(config['Results'], "01_evaluation/{asmID}/01B_QV-and-kmerMultiplicity/{asmID}.fasta"),
symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl")) symlink_merylDB=directory(os.path.join(config['Results'], "1_evaluation/{asmID}/04_merquryQVandKAT/merylDB_providedFor_{asmID}.meryl"))
threads: threads:
workflow.cores * 0.25 12
output: output:
os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.qv"), os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.qv"),
os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.completeness.stats"), os.path.join(config['Results'],"1_evaluation/{asmID}/04_merquryQVandKAT/{asmID}_merqOutput.completeness.stats"),
...@@ -235,6 +245,8 @@ rule genomescope2: ...@@ -235,6 +245,8 @@ rule genomescope2:
"../envs/genomescope.yaml" "../envs/genomescope.yaml"
log: log:
os.path.join(config['Results'],"1_evaluation/{asmID}/logs/{asmID}_k{kmer}_gscopelog.txt") os.path.join(config['Results'],"1_evaluation/{asmID}/logs/{asmID}_k{kmer}_gscopelog.txt")
threads:
1
shell: shell:
""" """
head -n 10000 {input.hist} > {params.cpHist} head -n 10000 {input.hist} > {params.cpHist}
...@@ -260,6 +272,8 @@ rule assemblyStats: ...@@ -260,6 +272,8 @@ rule assemblyStats:
path = os.path.join(config['Results'], "1_evaluation/{asmID}/02_assemblyStats/"), path = os.path.join(config['Results'], "1_evaluation/{asmID}/02_assemblyStats/"),
filename="{asmID}", filename="{asmID}",
given_size=lambda wildcards: expand("{genomeSize}", genomeSize=testDict[wildcards.asmID][4]) given_size=lambda wildcards: expand("{genomeSize}", genomeSize=testDict[wildcards.asmID][4])
threads:
1
shell: shell:
""" """
python {params.script} {input.assembly} {input.estGenome} {params.filename} {params.given_size} {output.scaffStats} {output.contStats} python {params.script} {input.assembly} {input.estGenome} {params.filename} {params.given_size} {output.scaffStats} {output.contStats}
...@@ -299,6 +313,8 @@ rule saveConfiguration_and_getKeyValues_kmer: ...@@ -299,6 +313,8 @@ rule saveConfiguration_and_getKeyValues_kmer:
gscopeSum=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_summary.txt"), gscopeSum=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_summary.txt"),
gscopeLog=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_log_plot.png"), gscopeLog=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_log_plot.png"),
gscopeLin=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_linear_plot.png") gscopeLin=os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/{asmID}_k{kmer}_linear_plot.png")
threads:
1
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"), # os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"),
# multiqc=os.path.join(config['Results'],"{sample}/5_31_Key_Results/{sample}_multiqc_report.html") # multiqc=os.path.join(config['Results'],"{sample}/5_31_Key_Results/{sample}_multiqc_report.html")
# aggregateTsv=os.path.join(config['Results'],"{sample}"+ "/individual_aggregated_results/aggregate.tsv") # aggregateTsv=os.path.join(config['Results'],"{sample}"+ "/individual_aggregated_results/aggregate.tsv")
...@@ -356,6 +372,8 @@ rule saveConfiguration_and_getKeyValues: ...@@ -356,6 +372,8 @@ rule saveConfiguration_and_getKeyValues:
# os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"), # os.path.join(config['Results'],"{sample}" + "/assemblyStats/{sample}_contig_stats.tsv"),
scaffStats=os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_scaffold_stats.tsv"), scaffStats=os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_scaffold_stats.tsv"),
contStats=os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_contig_stats.tsv") contStats=os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_contig_stats.tsv")
threads:
1
# os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"), # os.path.join(config['Results'],"{sample}" + "/QVstats_merylAndMerqury/logs/" + "{sample}" + "_meryl.log"),
# multiqc=os.path.join(config['Results'],"{sample}/5_31_Key_Results/{sample}_multiqc_report.html") # multiqc=os.path.join(config['Results'],"{sample}/5_31_Key_Results/{sample}_multiqc_report.html")
# aggregateTsv=os.path.join(config['Results'],"{sample}"+ "/individual_aggregated_results/aggregate.tsv") # aggregateTsv=os.path.join(config['Results'],"{sample}"+ "/individual_aggregated_results/aggregate.tsv")
...@@ -502,6 +520,8 @@ rule aggregateAllAssemblies: ...@@ -502,6 +520,8 @@ rule aggregateAllAssemblies:
# rows=os.path.join(config['Results'],"allAssemblies_keyResults/aggregate_rows.tsv"), # rows=os.path.join(config['Results'],"allAssemblies_keyResults/aggregate_rows.tsv"),
newSampleSheet=os.path.join(config['Results'],"1_evaluation/finalResults/savedSampleSheet.tsv"), newSampleSheet=os.path.join(config['Results'],"1_evaluation/finalResults/savedSampleSheet.tsv"),
newConfigFile=os.path.join(config['Results'],"1_evaluation/finalResults/savedConfig.yaml") newConfigFile=os.path.join(config['Results'],"1_evaluation/finalResults/savedConfig.yaml")
threads:
1
shell: shell:
""" """
cp {input.sampleSheet} {output.newSampleSheet} cp {input.sampleSheet} {output.newSampleSheet}
...@@ -524,7 +544,9 @@ rule makeReport: ...@@ -524,7 +544,9 @@ rule makeReport:
os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.completeness.stats"), os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.completeness.stats"),
os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/only_buscoScores_{asmID}.txt"), os.path.join(config['Results'], "1_evaluation/{asmID}/06_keyResults/only_buscoScores_{asmID}.txt"),
os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.fl.png"), os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.fl.png"),
os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.st.png") os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.spectra-cn.fl.png")
threads:
1
params: params:
"{asmID}", "{asmID}",
"{kmer}", "{kmer}",
...@@ -563,6 +585,8 @@ rule addFullTable: ...@@ -563,6 +585,8 @@ rule addFullTable:
results=os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv") results=os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv")
output: output:
os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md") os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md")
threads:
1
run: run:
import pandas as pd import pandas as pd
from tabulate import tabulate from tabulate import tabulate
...@@ -582,6 +606,8 @@ rule aggregateReport: ...@@ -582,6 +606,8 @@ rule aggregateReport:
endTableMD=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md") endTableMD=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown.md")
output: output:
os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md") os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md")
threads:
1
shell: shell:
""" """
cat {input.landingPage} {input.indivMD} {input.endTableMD} >> {output} cat {input.landingPage} {input.indivMD} {input.endTableMD} >> {output}
...@@ -597,6 +623,8 @@ rule makePDF: ...@@ -597,6 +623,8 @@ rule makePDF:
os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md") os.path.join(config['Results'],"1_evaluation/finalResults/FullMarkdown.md")
output: output:
os.path.join(config['Results'],"1_evaluation/finalResults/FULL_Report_PDF.pdf") os.path.join(config['Results'],"1_evaluation/finalResults/FULL_Report_PDF.pdf")
threads:
1
shell: shell:
""" """
pandoc -o {output} {input} pandoc -o {output} {input}
......
scripts/makePDF_indivMD.py
+ 2
− 2
View file @ bd5ee96d
...@@ -81,7 +81,7 @@ with open(snakemake.output[0], 'w') as outFile: ...@@ -81,7 +81,7 @@ with open(snakemake.output[0], 'w') as outFile:
print("### BUSCOv5 (database: ", params_buscoDB, ")", file=outFile) print("### BUSCOv5 (database: ", params_buscoDB, ")", file=outFile)
print("```", file=outFile) print("```", file=outFile)
for line in lines: for line in lines:
print(line, file=outFile) print(line, file=outFile)
print("```", file=outFile) print("```", file=outFile)
print("\\", file=outFile) print("\\", file=outFile)
print("", file=outFile) print("", file=outFile)
...@@ -89,7 +89,7 @@ with open(snakemake.output[0], 'w') as outFile: ...@@ -89,7 +89,7 @@ with open(snakemake.output[0], 'w') as outFile:
print("![](", kmer_flat, "){ width=38% }", file=outFile) print("![](", kmer_flat, "){ width=38% }", file=outFile)
print("\\", file=outFile) print("\\", file=outFile)
print("", file=outFile) print("", file=outFile)
print("### K-mer Multiplicity PRI and ALT (Flattened)", file=outFile) print("### K-mer Multiplicity PRI (Stacked)", file=outFile)
print("![](", kmer_stacked, "){ width=38% }", file=outFile) print("![](", kmer_stacked, "){ width=38% }", file=outFile)
print("\\", file=outFile) print("\\", file=outFile)
print("\\pagebreak", file=outFile) print("\\pagebreak", file=outFile)
......
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