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Commit d7f0b685 authored by james94's avatar james94
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fix bugs

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Snakefile
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View file @ d7f0b685
...@@ -36,7 +36,7 @@ def to_be_smrtTrimmed(userAnswer): ...@@ -36,7 +36,7 @@ def to_be_smrtTrimmed(userAnswer):
samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True) samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True)
if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns): if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns):
whichRule = "rules/illumina.smk" whichRule = "rules/illumina_05_11_21.smk"
samples=samples.reset_index() samples=samples.reset_index()
samples['readCounter'] = samples.groupby(['sample']).cumcount()+1 samples['readCounter'] = samples.groupby(['sample']).cumcount()+1
samples['readCounter'] = samples['readCounter'].astype(str) samples['readCounter'] = samples['readCounter'].astype(str)
...@@ -103,7 +103,7 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri ...@@ -103,7 +103,7 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri
ruleAll=[expand(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl"), sample=key, kmer=value1, trim10x=value2, trimAdapters=value3) for key, [value1, value2, value3] in testDict.items()] ruleAll=[expand(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl"), sample=key, kmer=value1, trim10x=value2, trimAdapters=value3) for key, [value1, value2, value3] in testDict.items()]
elif set(['sample', 'hifi_reads', 'meryl_kmer_size' ,'trimSMRTbell', 'fastQC']).issubset(samples.columns): elif set(['sample', 'hifi_reads', 'meryl_kmer_size' ,'trimSMRTbell', 'fastQC']).issubset(samples.columns):
whichRule = "rules/hifi.smk" whichRule = "rules/hifi_05_11_21.smk"
samples=samples.reset_index() samples=samples.reset_index()
samples['readCounter'] = samples.groupby(['sample']).cumcount()+1 samples['readCounter'] = samples.groupby(['sample']).cumcount()+1
samples['readCounter'] = samples['readCounter'].astype(str) samples['readCounter'] = samples['readCounter'].astype(str)
...@@ -171,10 +171,10 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size' ,'trimSMRTbell', 'fastQC']). ...@@ -171,10 +171,10 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size' ,'trimSMRTbell', 'fastQC']).
ruleAllQCFiles=[] ruleAllQCFiles=[]
if samples['fastQC'].str.contains('True').any(): if samples['fastQC'].str.contains('True').any():
ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{sample}.multiqcReport.html"), sample=key, smrtornot=value1) for key, [value1, value2] in testDictQC.items()] ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html"), sample=key, smrtornot=value1) for key, [value1, value2] in testDictQC.items()]
ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/03_merylDb/complete_hifi_{sample}_dB.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in testDict.items()] ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in testDict.items()]
elif set(['ID', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'genomeSize']).issubset(samples.columns): elif set(['ID', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'genomeSize']).issubset(samples.columns):
whichRule = "rules/run.smk" whichRule = "rules/run_05_11_21.smk"
samples['genomeSize'] = samples['genomeSize'].fillna(0) samples['genomeSize'] = samples['genomeSize'].fillna(0)
samples["genomeSize"] = pd.to_numeric(samples["genomeSize"]) samples["genomeSize"] = pd.to_numeric(samples["genomeSize"])
......
installGEP.yaml
+ 1
− 0
View file @ d7f0b685
...@@ -9,3 +9,4 @@ dependencies: ...@@ -9,3 +9,4 @@ dependencies:
- tabulate=0.8.7 - tabulate=0.8.7
- beautifulsoup4=4.9 - beautifulsoup4=4.9
- mamba=0.15.2 - mamba=0.15.2
- pandoc=2.16.1
rules/hifi_05_11_21.smk
+ 21
− 20
View file @ d7f0b685
...@@ -33,7 +33,7 @@ rule unzipHifi: ...@@ -33,7 +33,7 @@ rule unzipHifi:
input: input:
fastq=hifi_gzipped, fastq=hifi_gzipped,
output: output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
conda: conda:
...@@ -47,7 +47,7 @@ rule symlinkUnzippedHifi: ...@@ -47,7 +47,7 @@ rule symlinkUnzippedHifi:
input: input:
fastq=hifi_notgzipped, fastq=hifi_notgzipped,
output: output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
shell: shell:
...@@ -98,7 +98,7 @@ rule symlinkfornotSmartTrimmed: ...@@ -98,7 +98,7 @@ rule symlinkfornotSmartTrimmed:
input: input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
output: output:
outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq")) outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq")
shell: shell:
""" """
ln -s {input} {output.outputFile} ln -s {input} {output.outputFile}
...@@ -110,25 +110,28 @@ rule fastqc_hifi_SMRT_removed: ...@@ -110,25 +110,28 @@ rule fastqc_hifi_SMRT_removed:
params: params:
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/") folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/")
output: output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html") os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
threads: 1 threads: 1
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{readCounter}.{smrtornot}.FastQC.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log")
conda: conda:
"../envs/pigz.yaml" "../envs/pigz.yaml"
shell: shell:
"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}" """
mkdir {params.folder2out}
(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
"""
rule multiqc_hifi_SMRTremoved: rule multiqc_hifi_SMRTremoved:
input: input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], smrtornot=testDict[wildcards.sample][1]) lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], smrtornot=testDict[wildcards.sample][1])
params: params:
folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/"), folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/"),
filename="{sample}.{smrtornot}.multiqcReport.html" filename="{sample}.{smrtornot}.multiqcReport.html"
output: output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html") os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{sample}.{smrtornot}.multiqc.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.{smrtornot}.multiqc.log")
conda: conda:
"../envs/pigz.yaml" "../envs/pigz.yaml"
shell: shell:
...@@ -146,18 +149,17 @@ rule meryl_hifi_trimmed_count: ...@@ -146,18 +149,17 @@ rule meryl_hifi_trimmed_count:
kmer = "{kmer}" kmer = "{kmer}"
# path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/") # path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/")
threads: threads:
workflow.cores workflow.cores * 0.25
output: output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl")), directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl")),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
priority: priority:
10 10
conda: conda:
"../envs/merylMerq_2.yaml" "../envs/merylMerq_2.yaml"
shell: shell:
""" """
export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log} (meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log}
""" """
...@@ -165,24 +167,23 @@ rule meryl_hifi_build: ...@@ -165,24 +167,23 @@ rule meryl_hifi_build:
input: input:
# reads= rules.trimSMRTbell.output.outputFile # reads= rules.trimSMRTbell.output.outputFile
# lambda wildcards: expand(config['Results'],"{group}/alignment/{sample}.bam", group=wildcards.group, sample=GROUPS[wildcards.group] # lambda wildcards: expand(config['Results'],"{group}/alignment/{sample}.bam", group=wildcards.group, sample=GROUPS[wildcards.group]
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifi_reads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl"), sample=wildcards.sample, readCounter=d[wildcards.sample], kmer=testDict[wildcards.sample][0], smrtornot=testDict[wildcards.sample][1]) lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=d[wildcards.sample], kmer=testDict[wildcards.sample][0], smrtornot=testDict[wildcards.sample][1])
# reads=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{readCounter}" + "_hifi_dB.21.meryl") # reads=os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/" + "{readCounter}" + "_hifi_dB.21.meryl")
params: params:
kmer = "{kmer}" kmer = "{kmer}"
threads: threads:
workflow.cores workflow.cores * 0.5
output: output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}")), directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl")),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifi_reads/logs/{sample}_hifi_{smrtornot}.{kmer}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}_hifi_{smrtornot}.{kmer}.log")
priority: priority:
10 10
conda: conda:
"../envs/merylMerq_2.yaml" "../envs/merylMerq_2.yaml"
shell: shell:
""" """
export OMP_NUM_THREADS={threads} (meryl union-sum {input} output {output}) &> {log}
(meryl union-sum k={params.kmer} threads={threads} {input} output {output}) &> {log}
""" """
# #
# #
rules/illumina_05_11_21.smk
+ 19
− 9
View file @ d7f0b685
...@@ -40,7 +40,7 @@ rule unzipFasta_R1: ...@@ -40,7 +40,7 @@ rule unzipFasta_R1:
input: input:
assembly=R1_gzipped, assembly=R1_gzipped,
output: output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq")), os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log")
conda: conda:
...@@ -64,7 +64,7 @@ rule unzipFasta_R2: ...@@ -64,7 +64,7 @@ rule unzipFasta_R2:
input: input:
assembly=R2_gzipped, assembly=R2_gzipped,
output: output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq")), os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
conda: conda:
...@@ -88,10 +88,10 @@ rule symlinkUnzippedFasta_R2: ...@@ -88,10 +88,10 @@ rule symlinkUnzippedFasta_R2:
rule trim10xbarcodes: rule trim10xbarcodes:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"), read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq") # read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
output: output:
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq")), read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq")),
read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")) # read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
threads: threads:
workflow.cores * 0.125 workflow.cores * 0.125
log: log:
...@@ -101,12 +101,23 @@ rule trim10xbarcodes: ...@@ -101,12 +101,23 @@ rule trim10xbarcodes:
shell: shell:
""" """
(trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log} (trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log}
ln -s {input.read2} {output.read2}
""" """
# ln -s {input.read2} {output.read2}
rule trim10xbarcodesR2:
input:
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
output:
read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq"))
threads:
1
conda:
"../envs/pigz.yaml"
shell:
"""
ln -s {input.read2} {output.read2}
"""
...@@ -274,6 +285,5 @@ rule meryl_hifi_build: ...@@ -274,6 +285,5 @@ rule meryl_hifi_build:
"../envs/merylMerq_2.yaml" "../envs/merylMerq_2.yaml"
shell: shell:
""" """
export OMP_NUM_THREADS={threads} (meryl union-sum {input} output {output}) &> {log}
(meryl union-sum k={params.kmer} threads={threads} {input} output {output}) &> {log}
""" """
rules/run_05_11_21.smk
+ 3
− 3
View file @ d7f0b685
...@@ -87,7 +87,7 @@ rule busco5: ...@@ -87,7 +87,7 @@ 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 * 0.5 workflow.cores * 0.125
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"),
...@@ -149,7 +149,7 @@ rule merqury: ...@@ -149,7 +149,7 @@ 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 * 0.5 workflow.cores * 0.125
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"),
...@@ -529,7 +529,7 @@ rule makeReport: ...@@ -529,7 +529,7 @@ 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.spectra-cn.fl.png") os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.st.png")
params: params:
"{asmID}", "{asmID}",
"{kmer}", "{kmer}",
......
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