diff --git a/rules/build_hifi.smk b/rules/build_hifi.smk
index 6c616e58a4e259e71088011e4524aa41c7fb7493..7dca6234f94cd222dfb4c4e116daf402af4310aa 100644
--- a/rules/build_hifi.smk
+++ b/rules/build_hifi.smk
@@ -1,5 +1,7 @@
-localrules: symlinkUnzippedHifi, symlinkfornotSmartTrimmed, multiqc_hifi
+localrules: symlink_UnzippedFastq_hifi, \
+ symlink_noSMRTBellAdaptTrim_hifi, \
+ multiQC_hifi
@@ -20,62 +22,62 @@ def hifi_notgzipped(wildcards):
-rule unzipHifi:
+rule unzipFastq_hifi:
input:
fastq=hifi_gzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/pigzUnzip.{readCounter}.{smrtornot}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
- resource['unzipHifi']['threads']
+ resource['unzipFastq_hifi']['threads']
resources:
- mem_mb=resource['unzipHifi']['mem_mb'],
- time=resource['unzipHifi']['time'],
+ mem_mb=resource['unzipFastq_hifi']['mem_mb'],
+ time=resource['unzipFastq_hifi']['time'],
shell:
"""
pigz -p {threads} -c -d -k {input.fastq} > {output} 2> {log}
"""
-rule symlinkUnzippedHifi:
+rule symlink_UnzippedFastq_hifi:
input:
fastq=hifi_notgzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/pigzUnzip.{readCounter}.{smrtornot}.log")
container:
None
shell:
"""
ln -s {input.fastq} {output}
- echo "{input.fastq} no gzipped. Symlink created in place of expected decompressed file." > {log}
+ echo "{input.fastq} not gzipped. Symlink created in place of expected decompressed file." > {log}
"""
-rule trimSMRTbell:
+rule trimSMRTBellAdapters_hifi:
input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.smrtTrimmed.fastq"),
output:
outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.smrtTrimmed.fastq")
threads:
- resource['trimSMRTbell']['threads']
+ resource['trimSMRTBellAdapters_hifi']['threads']
resources:
- mem_mb=resource['trimSMRTbell']['mem_mb'],
- time=resource['trimSMRTbell']['time'],
+ mem_mb=resource['trimSMRTBellAdapters_hifi']['mem_mb'],
+ time=resource['trimSMRTBellAdapters_hifi']['time'],
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}_trimSMRTbell.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/trimSMRTbell.{readCounter}.log")
priority:
15
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"""
- (cutadapt -j {threads} -o {output.outputFile} {input} -b ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT -b ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --discard-trimmed) &> {log}
+ (cutadapt -j {threads} -o {output.outputFile} {input} -b AAAAAAAAAAAAAAAAAATTAACGGAGGAGGAGGA --overlap 35 -b ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --overlap 45 --revcomp -e 0.1 --discard-trimmed) &> {log}
"""
-rule symlinkfornotSmartTrimmed:
+rule symlink_noSMRTBellAdaptTrim_hifi:
input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
output:
@@ -87,7 +89,7 @@ rule symlinkfornotSmartTrimmed:
ln -s {input} {output.outputFile}
"""
-rule fastqc_hifi:
+rule fastQC_hifi:
input:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params:
@@ -95,20 +97,20 @@ rule fastqc_hifi:
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html")
threads:
- resource['trimSMRTbell']['threads']
+ resource['fastQC_hifi']['threads']
resources:
- mem_mb=resource['fastqc_hifi']['mem_mb'],
- time=resource['fastqc_hifi']['time'],
+ mem_mb=resource['fastQC_hifi']['mem_mb'],
+ time=resource['fastQC_hifi']['time'],
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/fastQC.hifi.{readCounter}.{smrtornot}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"""
(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
"""
-rule multiqc_hifi:
+rule multiQC_hifi:
input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], smrtornot=dictSamples[wildcards.sample][1])
params:
@@ -118,37 +120,37 @@ rule multiqc_hifi:
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html")
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.multiqc.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/multiQC.{sample}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"(multiqc {params.folder2qc} -o {params.folder2OUT} -n {params.filename}) &> {log}"
-rule meryl_hifi_count:
+rule merylCount_hifi:
input:
reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params:
kmer = "{kmer}"
threads:
- resource['meryl_hifi_count']['threads']
+ resource['merylCount_hifi']['threads']
resources:
- mem_mb=resource['meryl_hifi_count']['mem_mb'],
- time=resource['meryl_hifi_count']['time'],
+ mem_mb=resource['merylCount_hifi']['mem_mb'],
+ time=resource['merylCount_hifi']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))),
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/meryl_hifi_count.{readCounter}.{kmer}.{smrtornot}.log")
priority:
10
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
(meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log}
"""
-rule meryl_hifi_build:
+rule merylUnion_hifi:
input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], kmer=dictSamples[wildcards.sample][0], smrtornot=dictSamples[wildcards.sample][1])
params:
@@ -156,18 +158,18 @@ rule meryl_hifi_build:
removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/"),
removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/")
threads:
- resource['meryl_hifi_build']['threads']
+ resource['merylUnion_hifi']['threads']
resources:
- mem_mb=resource['meryl_hifi_build']['mem_mb'],
- time=resource['meryl_hifi_build']['time'],
+ mem_mb=resource['merylUnion_hifi']['mem_mb'],
+ time=resource['merylUnion_hifi']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl")),
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.meryl_hifi.{kmer}.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/meryl_hifi_combine.{sample}.{kmer}.log")
priority:
10
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
(meryl union-sum {input} output {output}) &> {log}
diff --git a/rules/build_illumina.smk b/rules/build_illumina.smk
index c1bb0e9eddc56bb9bf37a8987423d6ed80363956..0680f4a9db7a157cf824298b3311df1d764c459c 100644
--- a/rules/build_illumina.smk
+++ b/rules/build_illumina.smk
@@ -2,7 +2,13 @@
-localrules: symlinkUnzippedFastq_R1, symlinkUnzippedFastq_R2, symLink_trim10xbarcodes_notrimAdapt, symlinks_no10xwithAdaptTrim, symlinks_no10xOrAdaptTrim, symlink_trim10xbarcodesR2, multiqc_hifi
+localrules: symlink_UnzippedFastq_R1_illumina,\
+ symlink_UnzippedFastq_R2_illumina, \
+ symLink_Trim10xBarcodes_noSequencingAdaptTrim_illumina, \
+ symlink_No10xWithSequencingAdaptTrim_illumina, \
+ symlink_No10xOrSequencingAdaptTrim_illumina, \
+ symlink_Trim10xBarcodes_R2_illumina, \
+ multiQC_illumina
@@ -19,7 +25,7 @@ def R2_gzipped(wildcards):
def R2_notgzipped(wildcards):
return noGzip_R2.loc[(wildcards.sample, wildcards.readCounter), "Library_R2"]
-rule unzipFastq_R1:
+rule unzipFastq_R1_illumina:
input:
assembly=R1_gzipped,
output:
@@ -27,18 +33,18 @@ rule unzipFastq_R1:
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"),
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
- resource['unzipFastq_R1']['threads']
+ resource['unzipFastq_R1_illumina']['threads']
resources:
- mem_mb=resource['unzipFastq_R1']['mem_mb'],
- time=resource['unzipFastq_R1']['time']
+ mem_mb=resource['unzipFastq_R1_illumina']['mem_mb'],
+ time=resource['unzipFastq_R1_illumina']['time']
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
"""
-rule symlinkUnzippedFastq_R1:
+rule symlink_UnzippedFastq_R1_illumina:
input:
assembly=R1_notgzipped,
output:
@@ -50,7 +56,7 @@ rule symlinkUnzippedFastq_R1:
ln -s {input} {output}
"""
-rule unzipFastq_R2:
+rule unzipFastq_R2_illumina:
input:
assembly=R2_gzipped,
output:
@@ -58,18 +64,18 @@ rule unzipFastq_R2:
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
- resource['unzipFastq_R2']['threads']
+ resource['unzipFastq_R2_illumina']['threads']
resources:
- mem_mb=resource['unzipFastq_R2']['mem_mb'],
- time=resource['unzipFastq_R2']['time']
+ mem_mb=resource['unzipFastq_R2_illumina']['mem_mb'],
+ time=resource['unzipFastq_R2_illumina']['time']
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
"""
-rule symlinkUnzippedFastq_R2:
+rule symlink_UnzippedFastq_R2_illumina:
input:
assembly=R2_notgzipped,
output:
@@ -82,27 +88,27 @@ rule symlinkUnzippedFastq_R2:
"""
-rule trim10xbarcodes:
+rule trim10xBarcodes_illumina:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
threads:
- resource['trim10xbarcodes']['threads']
+ resource['trim10xBarcodes_illumina']['threads']
resources:
- mem_mb=resource['trim10xbarcodes']['mem_mb'],
- time=resource['trim10xbarcodes']['time']
+ mem_mb=resource['trim10xBarcodes_illumina']['mem_mb'],
+ time=resource['trim10xBarcodes_illumina']['time']
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.10xTrimmed.10BarcodeRemoval_Trimmomatic.{trimAdapters}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"""
(trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log}
"""
-rule symlink_trim10xbarcodesR2:
+rule symlink_Trim10xBarcodes_R2_illumina:
input:
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
output:
@@ -116,7 +122,7 @@ rule symlink_trim10xbarcodesR2:
-rule symLink_trim10xbarcodes_notrimAdapt:
+rule symLink_Trim10xBarcodes_noSequencingAdaptTrim_illumina:
input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.fastq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
@@ -131,7 +137,7 @@ rule symLink_trim10xbarcodes_notrimAdapt:
ln -s {input.read2} {output.read2}
"""
-rule symlinks_no10xOrAdaptTrim:
+rule symlink_No10xOrSequencingAdaptTrim_illumina:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
@@ -146,7 +152,7 @@ rule symlinks_no10xOrAdaptTrim:
ln -s {input.read2} {output.read2}
"""
-rule symlinks_no10xwithAdaptTrim:
+rule symlink_No10xWithSequencingAdaptTrim_illumina:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
@@ -161,7 +167,7 @@ rule symlinks_no10xwithAdaptTrim:
ln -s {input.read2} {output.read2}
"""
-rule trimAdapters:
+rule trimSequencingAdapters_illumina:
input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.fastq"),
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
@@ -172,20 +178,20 @@ rule trimAdapters:
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.fq")),
read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
threads:
- resource['trimAdapters']['threads']
+ resource['trimSequencingAdapters_illumina']['threads']
resources:
- mem_mb=resource['trimAdapters']['mem_mb'],
- time=resource['trimAdapters']['time'],
+ mem_mb=resource['trimSequencingAdapters_illumina']['mem_mb'],
+ time=resource['trimSequencingAdapters_illumina']['time'],
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.AdaptTrimmed_tGalore.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"""
(trim_galore -j {threads} --basename {params.r1_prefix} --dont_gzip --length 65 -o {params.outputDir} --paired {input.read1} {input.read2}) &> {log}
"""
-rule fastqc_Illumina:
+rule fastQC_illumina:
input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
@@ -197,16 +203,16 @@ rule fastqc_Illumina:
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log")
threads:
- resource['fastqc_Illumina']['threads']
+ resource['fastQC_illumina']['threads']
resources:
- mem_mb=resource['fastqc_Illumina']['mem_mb'],
- time=resource['fastqc_Illumina']['time'],
+ mem_mb=resource['fastQC_illumina']['mem_mb'],
+ time=resource['fastQC_illumina']['time'],
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}"
-rule multiqc_hifi:
+rule multiQC_illumina:
input:
read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2])
@@ -219,22 +225,22 @@ rule multiqc_hifi:
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.multiqc.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell:
"(multiqc {params.folder2qc} -o {params.folder2out} -n {params.filename}) &> {log}"
-rule meryl_R1:
+rule merylCount_R1_illumina:
input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
params:
kmer = "{kmer}",
threads:
- resource['meryl_R1']['threads']
+ resource['merylCount_R1_illumina']['threads']
resources:
- mem_mb=resource['meryl_R1']['mem_mb'],
- time=resource['meryl_R1']['time'],
+ mem_mb=resource['merylCount_R1_illumina']['mem_mb'],
+ time=resource['merylCount_R1_illumina']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl")))
log:
@@ -242,23 +248,23 @@ rule meryl_R1:
priority:
10
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
"""
-rule meryl_R2:
+rule merylCount_R2_illumina:
input:
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
params:
kmer = "{kmer}",
threads:
- resource['meryl_R2']['threads']
+ resource['merylCount_R2_illumina']['threads']
resources:
- mem_mb=resource['meryl_R2']['mem_mb'],
- time=resource['meryl_R2']['time'],
+ mem_mb=resource['merylCount_R2_illumina']['mem_mb'],
+ time=resource['merylCount_R2_illumina']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl")))
log:
@@ -266,7 +272,7 @@ rule meryl_R2:
priority:
10
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
export OMP_NUM_THREADS={threads}
@@ -274,7 +280,7 @@ rule meryl_R2:
"""
-rule meryl_illumina_build:
+rule merylUnion_illumina:
input:
# removeReads1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
# removeReads2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
@@ -286,10 +292,10 @@ rule meryl_illumina_build:
kmer = "{kmer}",
path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/")
threads:
- resource['meryl_illumina_build']['threads']
+ resource['merylUnion_illumina']['threads']
resources:
- mem_mb=resource['meryl_illumina_build']['mem_mb'],
- time=resource['meryl_illumina_build']['time'],
+ mem_mb=resource['merylUnion_illumina']['mem_mb'],
+ time=resource['merylUnion_illumina']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/complete_illumina.{sample}.{kmer}.meryl")),
log:
@@ -297,7 +303,7 @@ rule meryl_illumina_build:
priority:
10
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
export OMP_NUM_THREADS={threads}
diff --git a/rules/evaluate.smk b/rules/evaluate.smk
index c6813378d95810d885b7b141fe7ddb81ed05fbac..2867bd0b5a8b9bbc8e920538262399fb2f3adb54 100644
--- a/rules/evaluate.smk
+++ b/rules/evaluate.smk
@@ -5,41 +5,42 @@ def merylDB(wildcards):
return samples.loc[(wildcards.asmID), "merylDB"]
-localrules: symlinkUnzippedHiC_R1, \
- symlinkUnzippedHiC_R2, \
- symlinkUnzippedFasta_PRI, \
- symlinkUnzippedFasta_ALT, \
+localrules: symlink_UnzippedFastq_R1_HiC, \
+ symlink_UnzippedFastq_R2_HiC, \
+ symlink_UnzippedFasta_PRI, \
+ symlink_UnzippedFasta_ALT, \
# symlinkMerylDB, \
# moveBuscoOutputs, \
- saveConfiguration_and_getKeyValues_kmer, \
- saveConfiguration_and_getKeyValues, \
- aggregateAllAssemblies, \
- makeReport, \
- pretextMaps2md, \
- addFullTable, \
- aggregateReport, \
- fullTable_heatmap_external_create, \
- fullTable_heatmap_external_createPDF, \
- fullTable_heatmap_internal_create, \
- makePDF_combine
+ copyKeyResults_GenomeScope2Profiles, \
+ copyKeyResults, \
+ saveConfigurationAndSampleSheet_createComparisonTablesTSV, \
+ IndividualKeyResults_createMD, \
+ PretextMaps_createMD, \
+ ComparisonTables_createMD, \
+ ReportWithoutComparisonTables_createMD, \
+ ReportWithoutComparisonTables_createPDF, \
+ ComparisonTablesColoured_createHTML, \
+ ComparisonTables_createPDF, \
+ ComparisonTablesGradient_createHTML, \
+ COMBINE_ALL_PDFS
def HiC_R1_gzipped(wildcards):
return yesGzip_HiC_R1.loc[(wildcards.asmID), "HiC_R1"]
-rule unzipHiC_R1:
+rule unzipFastq_R1_HiC:
input:
assembly=HiC_R1_gzipped,
output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.fastq")),
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.R1.pigzUnzip.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip..HiC.R1.{asmID}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
- resource['unzipHiC_R1']['threads']
+ resource['unzipFastq_R1_HiC']['threads']
resources:
- mem_mb=resource['unzipHiC_R1']['mem_mb'],
- time=resource['unzipHiC_R1']['time'],
+ mem_mb=resource['unzipFastq_R1_HiC']['mem_mb'],
+ time=resource['unzipFastq_R1_HiC']['time'],
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
@@ -48,7 +49,7 @@ rule unzipHiC_R1:
def HiC_R1_unzipped(wildcards):
return noGzip_HiC_R1.loc[(wildcards.asmID), "HiC_R1"]
-rule symlinkUnzippedHiC_R1:
+rule symlink_UnzippedFastq_R1_HiC:
input:
assembly=HiC_R1_unzipped,
output:
@@ -64,20 +65,20 @@ rule symlinkUnzippedHiC_R1:
def HiC_R2_gzipped(wildcards):
return yesGzip_HiC_R2.loc[(wildcards.asmID), "HiC_R2"]
-rule unzipHiC_R2:
+rule unzipFastq_R2_HiC:
input:
assembly=HiC_R2_gzipped,
output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R2.fastq")),
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.R2.pigzUnzip.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip..HiC.R2.{asmID}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
- resource['unzipHiC_R2']['threads']
+ resource['unzipFastq_R2_HiC']['threads']
resources:
- mem_mb=resource['unzipHiC_R2']['mem_mb'],
- time=resource['unzipHiC_R2']['time']
+ mem_mb=resource['unzipFastq_R2_HiC']['mem_mb'],
+ time=resource['unzipFastq_R2_HiC']['time']
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
@@ -86,7 +87,7 @@ rule unzipHiC_R2:
def HiC_R2_unzipped(wildcards):
return noGzip_HiC_R2.loc[(wildcards.asmID), "HiC_R2"]
-rule symlinkUnzippedHiC_R2:
+rule symlink_UnzippedFastq_R2_HiC:
input:
assembly=HiC_R2_unzipped,
output:
@@ -102,7 +103,7 @@ rule symlinkUnzippedHiC_R2:
-rule pretext_index_PRI_asm:
+rule indexFasta_PRI:
input:
assemblyPRI=os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
output:
@@ -113,21 +114,21 @@ rule pretext_index_PRI_asm:
os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta.pac"),
os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta.fai")
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.PRI.indexing.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/indexASM.PRI.{asmID}.log")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_index_PRI_asm']['threads']
+ resource['indexFasta_PRI']['threads']
resources:
- mem_mb=resource['pretext_index_PRI_asm']['mem_mb'],
- time=resource['pretext_index_PRI_asm']['time']
+ mem_mb=resource['indexFasta_PRI']['mem_mb'],
+ time=resource['indexFasta_PRI']['time']
shell:
"""
(bwa-mem2 index {input.assemblyPRI}) &> {log}
(samtools faidx {input.assemblyPRI}) &>> {log}
"""
-rule pretext_fastq2bam_R1:
+rule convertFastqTObam_R1_HiC:
input:
HiC_R1=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.fastq"),
assembly=os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
@@ -140,20 +141,20 @@ rule pretext_fastq2bam_R1:
output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.bam"))
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_fastq2bam_R1']['threads']
+ resource['convertFastqTObam_R1_HiC']['threads']
resources:
- mem_mb=resource['pretext_fastq2bam_R1']['mem_mb'],
- time=resource['pretext_fastq2bam_R1']['time']
+ mem_mb=resource['convertFastqTObam_R1_HiC']['mem_mb'],
+ time=resource['convertFastqTObam_R1_HiC']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.fastq2bam.R1.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/fastq2bam.HiC.R1.{asmID}.log")
shell:
"""
(bwa-mem2 mem -t {threads} -B8 {input.assembly} {input.HiC_R1} | samtools view -Sb - > {output}) &> {log}
"""
-rule pretext_fastq2bam_R2:
+rule convertFastqTObam_R2_HiC:
input:
HiC_R2=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R2.fastq"),
assembly=os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
@@ -166,20 +167,20 @@ rule pretext_fastq2bam_R2:
output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R2.bam"))
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_fastq2bam_R2']['threads']
+ resource['convertFastqTObam_R2_HiC']['threads']
resources:
- mem_mb=resource['pretext_fastq2bam_R2']['mem_mb'],
- time=resource['pretext_fastq2bam_R2']['time']
+ mem_mb=resource['convertFastqTObam_R2_HiC']['mem_mb'],
+ time=resource['convertFastqTObam_R2_HiC']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.fastq2bam.R2.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/fastq2bam.HiC.R2.{asmID}.log")
shell:
"""
(bwa-mem2 mem -t {threads} -B8 {input.assembly} {input.HiC_R2} | samtools view -Sb - > {output}) &> {log}
"""
-rule pretext_filter_5primeEnd_R1:
+rule filter5PrimeEnd_R1_HiC:
input:
HiC_R1_bam=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.bam"),
assembly=os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
@@ -194,20 +195,20 @@ rule pretext_filter_5primeEnd_R1:
params:
script=os.path.join(workflow.basedir, "scripts/process_HiC/filter_five_end.pl")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_filter_5primeEnd_R1']['threads']
+ resource['filter5PrimeEnd_R1_HiC']['threads']
resources:
- mem_mb=resource['pretext_filter_5primeEnd_R1']['mem_mb'],
- time=resource['pretext_filter_5primeEnd_R1']['time']
+ mem_mb=resource['filter5PrimeEnd_R1_HiC']['mem_mb'],
+ time=resource['filter5PrimeEnd_R1_HiC']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.filter5end.R1.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/filtered.HiC.R1.{asmID}.log")
shell:
"""
(samtools view -h {input.HiC_R1_bam}| perl {params.script} | samtools view -@{threads} -Sb - > {output}) &> {log}
"""
-rule pretext_filter_5primeEnd_R2:
+rule filter5PrimeEnd_R2_HiC:
input:
HiC_R2_bam=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R2.bam"),
assembly=os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
@@ -222,21 +223,21 @@ rule pretext_filter_5primeEnd_R2:
params:
script=os.path.join(workflow.basedir, "scripts/process_HiC/filter_five_end.pl")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_filter_5primeEnd_R2']['threads']
+ resource['filter5PrimeEnd_R2_HiC']['threads']
resources:
- mem_mb=resource['pretext_filter_5primeEnd_R2']['mem_mb'],
- time=resource['pretext_filter_5primeEnd_R2']['time']
+ mem_mb=resource['filter5PrimeEnd_R2_HiC']['mem_mb'],
+ time=resource['filter5PrimeEnd_R2_HiC']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.filter5end.R2.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/filtered.HiC.R1.{asmID}.log")
shell:
"""
(samtools view -h {input.HiC_R2_bam}| perl {params.script} | samtools view -@{threads} -Sb - > {output}) &> {log}
"""
-rule pretext_filtered_combine:
+rule pairAndCombineFiltered_HiC:
input:
R1=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.FILTERED.bam"),
R2=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R2.FILTERED.bam")
@@ -245,39 +246,39 @@ rule pretext_filtered_combine:
params:
script=os.path.join(workflow.basedir, "scripts/process_HiC/two_read_bam_combiner.pl")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_filtered_combine']['threads']
+ resource['pairAndCombineFiltered_HiC']['threads']
resources:
- mem_mb=resource['pretext_filtered_combine']['mem_mb'],
- time=resource['pretext_filtered_combine']['time']
+ mem_mb=resource['pairAndCombineFiltered_HiC']['mem_mb'],
+ time=resource['pairAndCombineFiltered_HiC']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.COMBINED.FILTERED.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/combine.filtered.HiC.{asmID}.log")
shell:
"""
(perl {params.script} {input.R1} {input.R2} | samtools view -@{threads} -Sb > {output}) &>{log}
"""
-rule pretext_map:
+rule pretextMap:
input:
HiC_alignment=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED.bam")
output:
pretextFile=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED.pretext")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_map']['threads']
+ resource['pretextMap']['threads']
resources:
- mem_mb=resource['pretext_map']['mem_mb'],
- time=resource['pretext_map']['time']
+ mem_mb=resource['pretextMap']['mem_mb'],
+ time=resource['pretextMap']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.COMBINED.FILTERED.PretextMap.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/PretextMap.{asmID}.log")
shell:
"""
(samtools view -h {input.HiC_alignment} | PretextMap -o {output.pretextFile} --sortby length --mapq 10) &> {log}
"""
-rule pretext_snapshot:
+rule pretextSnapshot:
input:
pretextFile=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED.pretext")
output:
@@ -285,14 +286,14 @@ rule pretext_snapshot:
params:
outDirectory=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/")
conda:
- os.path.join(workflow.basedir, "envs/pretext.yaml")
+ os.path.join(workflow.basedir, "envs/HiC_CONTACT_MAPS.yaml")
threads:
- resource['pretext_snapshot']['threads']
+ resource['pretextSnapshot']['threads']
resources:
- mem_mb=resource['pretext_snapshot']['mem_mb'],
- time=resource['pretext_snapshot']['time']
+ mem_mb=resource['pretextSnapshot']['mem_mb'],
+ time=resource['pretextSnapshot']['time']
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.HiC.COMBINED.FILTERED.PretextSnapshot.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/PretextSnapshot.{asmID}.log")
shell:
"""
(PretextSnapshot -m {input.pretextFile} -o {params.outDirectory}) &> {log}
@@ -310,9 +311,9 @@ rule unzipFasta_PRI:
output:
os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.PRI.fasta"),
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.PRI.pigzUnzip.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.PRI.{asmID}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
resource['unzipFasta_PRI']['threads']
resources:
@@ -326,7 +327,7 @@ rule unzipFasta_PRI:
def PRI_asm_unzipped(wildcards):
return noGzip_PRI.loc[(wildcards.asmID), "PRI_asm"]
-rule symlinkUnzippedFasta_PRI:
+rule symlink_UnzippedFasta_PRI:
input:
assembly=PRI_asm_unzipped,
output:
@@ -349,7 +350,7 @@ rule unzipFasta_ALT:
output:
os.path.join(config['Results'], "1_evaluation/{asmID}/ASSEMBLY_FASTAS/{asmID}.ALT.fasta"),
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}.ALT.pigzUnzip.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.ALT.{asmID}.log")
conda:
os.path.join(workflow.basedir, "envs/pigz.yaml")
threads:
@@ -366,7 +367,7 @@ rule unzipFasta_ALT:
def ALT_asm_unzipped(wildcards):
return noGzip_ALT.loc[(wildcards.asmID), "ALT_asm"]
-rule symlinkUnzippedFasta_ALT:
+rule symlink_UnzippedFasta_ALT:
input:
assembly=ALT_asm_unzipped,
output:
@@ -425,11 +426,11 @@ rule merqury:
os.path.join(config['Results'],"1_evaluation/{asmID}/QV.KMER-COMPLETENESS.CN-SPECTRA/{asmID}_merqOutput.spectra-cn.fl.png"),
os.path.join(config['Results'],"1_evaluation/{asmID}/QV.KMER-COMPLETENESS.CN-SPECTRA/merylDB_providedFor_{asmID}.hist")
log:
- os.path.join(config['Results'],"1_evaluation/{asmID}/logs/{asmID}_merqury.log")
+ os.path.join(config['Results'],"1_evaluation/{asmID}/logs/merqury.{asmID}.log")
priority:
3
conda:
- os.path.join(workflow.basedir, "envs/merylMerq_2.yaml")
+ os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
ln -s {input.merylDB_provided} {params.symlink_merylDB}
@@ -459,9 +460,9 @@ rule busco5:
output:
os.path.join(config['Results'], "1_evaluation/{asmID}/BUSCOs/{asmID}/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"),
conda:
- os.path.join(workflow.basedir, "envs/busco_and_assembly.yaml")
+ os.path.join(workflow.basedir, "envs/BUSCO.yaml")
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/{asmID}_busco5.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/busco5.{asmID}.log")
priority:
20
shell:
@@ -474,7 +475,7 @@ rule busco5:
-rule genomescope2:
+rule GenomeScope2Profiles:
input:
hist=os.path.join(config['Results'],"1_evaluation/{asmID}/QV.KMER-COMPLETENESS.CN-SPECTRA/merylDB_providedFor_{asmID}.hist"),
params:
@@ -488,14 +489,14 @@ rule genomescope2:
linearPlot=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_linear_plot.png"),
estimatedSize=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_sizeEst.txt")
conda:
- os.path.join(workflow.basedir, "envs/genomescope.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_R_SCRIPTS.yaml")
log:
- os.path.join(config['Results'],"1_evaluation/{asmID}/logs/{asmID}_k{kmer}_gscopelog.txt")
+ os.path.join(config['Results'],"1_evaluation/{asmID}/logs/genomescopeProfiles.{asmID}.{kmer}.log")
threads:
- resource['genomescope2']['threads']
+ resource['GenomeScope2Profiles']['threads']
resources:
- mem_mb=resource['genomescope2']['mem_mb'],
- time=resource['genomescope2']['time']
+ mem_mb=resource['GenomeScope2Profiles']['mem_mb'],
+ time=resource['GenomeScope2Profiles']['time']
shell:
"""
head -n 10000 {input.hist} > {params.cpHist}
@@ -516,7 +517,9 @@ rule assemblyStats:
filename="{asmID}",
given_size=lambda wildcards: expand("{genomeSize}", genomeSize=dictSamples[wildcards.asmID][4])
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
+ log:
+ os.path.join(config['Results'],"1_evaluation/{asmID}/logs/assemblyStats.{asmID}.log")
threads:
resource['assemblyStats']['threads']
resources:
@@ -524,13 +527,13 @@ rule assemblyStats:
time=resource['assemblyStats']['time']
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}) &> {log}
"""
-rule saveConfiguration_and_getKeyValues_kmer:
+rule copyKeyResults_GenomeScope2Profiles:
input:
gscopeSum=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"),
gscopeLog=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"),
@@ -551,11 +554,11 @@ rule saveConfiguration_and_getKeyValues_kmer:
-rule saveConfiguration_and_getKeyValues:
+rule copyKeyResults:
input:
gscopeSum=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
- gscopeLog=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
- gscopeLin=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_linear_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
+ # gscopeLog=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
+ # gscopeLin=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_linear_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
busco=os.path.join(config['Results'], "1_evaluation/{asmID}/BUSCOs/{asmID}/short_summary.specific." + buscoDataBaseName + "_odb10.{asmID}.txt"),
qv=os.path.join(config['Results'],"1_evaluation/{asmID}/QV.KMER-COMPLETENESS.CN-SPECTRA/{asmID}_merqOutput.qv"),
completeness=os.path.join(config['Results'],"1_evaluation/{asmID}/QV.KMER-COMPLETENESS.CN-SPECTRA/{asmID}_merqOutput.completeness.stats"),
@@ -625,7 +628,7 @@ rule saveConfiguration_and_getKeyValues:
rm {params.rowNames} {params.keyValues}
"""
-rule aggregateAllAssemblies:
+rule saveConfigurationAndSampleSheet_createComparisonTablesTSV:
input:
allResults=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"), asmID=list(dictSamples.keys())),
sampleSheet= config['samplesTSV'],
@@ -647,9 +650,9 @@ rule aggregateAllAssemblies:
sed -i 's/,//g' {output.results}
"""
-rule makeReport:
+rule IndividualKeyResults_createMD:
input:
- os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedResults.tsv"),
+ os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"),
lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_log_plot.png"),asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_linear_plot.png"),asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_merqOutput.qv"),
@@ -658,7 +661,7 @@ rule makeReport:
os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_merqOutput.{asmID}.PRI.spectra-cn.st.png"),
os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_merqOutput.spectra-cn.st.png")
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
params:
"{asmID}",
"{kmer}",
@@ -670,7 +673,7 @@ rule makeReport:
-rule pretextMaps2md:
+rule PretextMaps_createMD:
input:
PretextMap=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED_FullMap.png")
output:
@@ -679,22 +682,22 @@ rule pretextMaps2md:
params:
assemblyName='{asmID}'
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
script:
os.path.join(workflow.basedir, "scripts/report/pretextMapsToMarkdown.py")
-rule addFullTable:
+rule ComparisonTables_createMD:
input:
results=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.tsv")
output:
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.md"),
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
script:
os.path.join(workflow.basedir, "scripts/report/addFullTableForReport.py")
-rule fullTable_heatmap_external_create:
+rule ComparisonTablesColoured_createHTML:
input:
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
params:
@@ -707,11 +710,11 @@ rule fullTable_heatmap_external_create:
# mem_mb=resource['fullTable_heatmap_external_create']['mem_mb'],
# time=resource['fullTable_heatmap_external_create']['time']
conda:
- os.path.join(workflow.basedir, "envs/genomescope.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_R_SCRIPTS.yaml")
script:
os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_external.R")
-rule fullTable_heatmap_internal_create:
+rule ComparisonTablesGradient_createHTML:
input:
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
params:
@@ -724,18 +727,18 @@ rule fullTable_heatmap_internal_create:
# mem_mb=resource['fullTable_heatmap_external_create']['mem_mb'],
# time=resource['fullTable_heatmap_external_create']['time']
conda:
- os.path.join(workflow.basedir, "envs/genomescope.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_R_SCRIPTS.yaml")
script:
os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_internalComparison.R")
-rule fullTable_heatmap_external_createPDF:
+rule ComparisonTables_createPDF:
input:
coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.html"),
gradient=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_GRADIENT.html")
params:
css=os.path.join(workflow.basedir, "scripts/report/tableOnSamePage.css")
log:
- os.path.join(config['Results'], "1_evaluation/logs/fullTable_heatmap_createPDF_pandoc.log")
+ os.path.join(config['Results'], "1_evaluation/logs/ComparisonTables_createPDF.log")
output:
coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.pdf"),
gradient=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_GRADIENT.pdf")
@@ -745,7 +748,7 @@ rule fullTable_heatmap_external_createPDF:
# mem_mb=resource['fullTable_heatmap_external_createPDF']['mem_mb'],
# time=resource['fullTable_heatmap_external_createPDF']['time']
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
shell:
"""
(pandoc -V papersize:a3 -V margin-top=1.5cm -V margin-left=1.5cm -V margin-right=0 -V margin-bottom=0 -c {params.css} -o {output.coloured} --pdf-engine=wkhtmltopdf {input.coloured}) &>> {log}
@@ -753,7 +756,7 @@ rule fullTable_heatmap_external_createPDF:
-o {output.gradient} --pdf-engine=wkhtmltopdf --pdf-engine-opt="-O" --pdf-engine-opt="Landscape" {input.gradient}) &>> {log}
"""
-rule aggregateReport:
+rule ReportWithoutComparisonTables_createMD:
input:
indivMD=[expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_markdownForReport.md"), asmID=key, kmer=value5) for key, [value1, value2, value3, value4, value5, value6, value7, value8, value9, value10, value11, value12, value13, value14, value15, value16] in dictSamples.items()],
landingPage=os.path.join(workflow.basedir, "scripts/report/reportLandingPage.md"),
@@ -772,7 +775,7 @@ rule aggregateReport:
# cat {input.landingPageTABLE} {input.endTableMD} >> {output.endTableMD}
-rule makePDF:
+rule ReportWithoutComparisonTables_createPDF:
input:
md_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.md"),
# md_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown_wPreamble.md")
@@ -780,21 +783,21 @@ rule makePDF:
pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.pdf"),
# pdf_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
log:
- os.path.join(config['Results'], "1_evaluation/logs/MAKEPDF_pandoc.log")
+ os.path.join(config['Results'], "1_evaluation/logs/ReportWithoutComparisonTables_createPDF.log")
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
- threads:
- resource['makePDF']['threads']
- resources:
- mem_mb=resource['makePDF']['mem_mb'],
- time=resource['makePDF']['time']
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
+ # threads:
+ # resource['ReportWithoutComparisonTables_createPDF']['threads']
+ # resources:
+ # mem_mb=resource['ReportWithoutComparisonTables_createPDF']['mem_mb'],
+ # time=resource['ReportWithoutComparisonTables_createPDF']['time']
shell:
"""
(pandoc -o {output.pdf_report} {input.md_report} --pdf-engine=tectonic) &>> {log}
"""
# (pandoc -o {output.pdf_comparison_table} {input.md_comparison_table} --pdf-engine=tectonic) &>> {log}
-rule makePDF_combine:
+rule COMBINE_ALL_PDFS:
input:
pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.pdf"),
coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.pdf"),
@@ -804,9 +807,9 @@ rule makePDF_combine:
pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/FINAL_REPORT.pdf"),
# pdf_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
log:
- os.path.join(config['Results'], "1_evaluation/logs/MAKEPDF_combine.log")
+ os.path.join(config['Results'], "1_evaluation/logs/COMBINE_ALL_PDFS.log")
conda:
- os.path.join(workflow.basedir, "envs/python_scripts.yaml")
+ os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
# threads:
# resource['makePDF']['threads']
# resources: