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Log and benchmark fixes #114

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merged 6 commits into from
Aug 17, 2023
Merged

Log and benchmark fixes #114

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bff0810
Logs are now in outdir and are referenced in rules
supermaxiste Aug 11, 2023
b6223a1
Fixed double backslash issue in log path
supermaxiste Aug 11, 2023
6fd7bd6
Fix build eagle logs and modified GH actions for PRs only
supermaxiste Aug 11, 2023
2402b9d
Fix typo
supermaxiste Aug 11, 2023
c592577
log only stderr for cutadapt
supermaxiste Aug 11, 2023
a9eb1ce
Only log stderr
supermaxiste Aug 11, 2023
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1 change: 0 additions & 1 deletion .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@ name: ARPEGGIO_run
# events but only for the master branch. Added trigger to publishhed and created
# releases as well
on:
push:
pull_request:
branches: [ master ]
release:
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28 changes: 14 additions & 14 deletions rules/alignment.smk
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Expand Up @@ -12,17 +12,17 @@ rule bismark_prepare_genome_1:
output:
control=f"{GENOME_1}Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa",
log:
f"logs/bismark_prepare_genome_1.log",
f"{OUTPUT_DIR}logs/bismark_prepare_genome_1.log",
params:
genome1=lambda w, output: os.path.split(
os.path.split(os.path.split(output.control)[0])[0]
)[0],
benchmark:
f"{OUTPUT_DIR}benchmark/prepare_genome.txt"
f"{OUTPUT_DIR}benchmark/prepare_genome_1.txt"
conda:
"../envs/environment.yaml"
shell:
"bismark_genome_preparation {params.genome1}"
"bismark_genome_preparation {params.genome1} 2> {log}"


## Run Bismark to prepare synthetic bisulfite converted genomes
Expand All @@ -32,17 +32,17 @@ rule bismark_prepare_genome_2:
output:
control=f"{GENOME_2}Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa",
log:
f"logs/bismark_prepare_genome_2.log",
f"{OUTPUT_DIR}logs/bismark_prepare_genome_2.log",
params:
genome2=lambda w, output: os.path.split(
os.path.split(os.path.split(output.control)[0])[0]
)[0],
benchmark:
f"{OUTPUT_DIR}benchmark/prepare_genome.txt"
f"{OUTPUT_DIR}benchmark/prepare_genome_2.txt"
conda:
"../envs/environment.yaml"
shell:
"bismark_genome_preparation {params.genome2}"
"bismark_genome_preparation {params.genome2} 2> {log}"


## Run Bismark to perform alignment to the first parental genome (GENOME_PARENT_1) if reads are single-end.
Expand All @@ -62,7 +62,7 @@ rule bismark_alignment_SE_1:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/{{sample}}_1/1.{{sample}}_bismark_bt2_SE_report.txt",
log:
f"logs/bismark_alignment_{{sample}}_SE_1.log",
f"{OUTPUT_DIR}logs/bismark_alignment_{{sample}}_SE_1.log",
params:
output=lambda w, output: os.path.split(output.sample)[0],
genome1=lambda w, input: os.path.split(
Expand All @@ -76,7 +76,7 @@ rule bismark_alignment_SE_1:
"../envs/environment.yaml"
threads: CORES
shell:
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} -o {params.output} --temp_dir {params.output} --genome {params.genome1} {input.fastq}"
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} -o {params.output} --temp_dir {params.output} --genome {params.genome1} {input.fastq} 2> {log}"


## Run Bismark to perform alignment to the second parental genome (GENOME_PARENT_2) if reads are single-end.
Expand All @@ -96,7 +96,7 @@ rule bismark_alignment_SE_2:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/{{sample}}_2/2.{{sample}}_bismark_bt2_SE_report.txt",
log:
f"logs/bismark_alignment_{{sample}}_SE_2.log",
f"{OUTPUT_DIR}logs/bismark_alignment_{{sample}}_SE_2.log",
params:
output=lambda w, output: os.path.split(output.sample)[0],
genome2=lambda w, input: os.path.split(
Expand All @@ -110,7 +110,7 @@ rule bismark_alignment_SE_2:
"../envs/environment.yaml"
threads: CORES
shell:
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} -o {params.output} --temp_dir {params.output} --genome {params.genome2} {input.fastq}"
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} -o {params.output} --temp_dir {params.output} --genome {params.genome2} {input.fastq} 2> {log}"


## Run Bismark to perform alignment to the first parental genome (GENOME_PARENT_1) if reads are paired-end.
Expand All @@ -133,7 +133,7 @@ rule bismark_alignment_PE_1:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/{{sample}}_1/1.{{sample}}_{str(config['PAIR_1'])}_bismark_bt2_PE_report.txt",
log:
f"logs/bismark_alignment_{{sample}}_PE_1.log",
f"{OUTPUT_DIR}logs/bismark_alignment_{{sample}}_PE_1.log",
params:
output=lambda w, output: os.path.split(output.sample)[0],
genome1=lambda w, input: os.path.split(
Expand All @@ -147,7 +147,7 @@ rule bismark_alignment_PE_1:
"../envs/environment.yaml"
threads: CORES
shell:
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} --genome {params.genome1} -1 {input.fastq1} -2 {input.fastq2} -o {params.output} --temp_dir {params.output}"
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} --genome {params.genome1} -1 {input.fastq1} -2 {input.fastq2} -o {params.output} --temp_dir {params.output} 2> {log}"


## Run Bismark to perform alignment to the second parental genome (GENOME_PARENT_2) if reads are paired-end.
Expand All @@ -170,7 +170,7 @@ rule bismark_alignment_PE_2:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/{{sample}}_2/2.{{sample}}_{str(config['PAIR_1'])}_bismark_bt2_PE_report.txt",
log:
f"logs/bismark_alignment_{{sample}}_PE_2.log",
f"{OUTPUT_DIR}logs/bismark_alignment_{{sample}}_PE_2.log",
params:
output=lambda w, output: os.path.split(output.sample)[0],
genome2=lambda w, input: os.path.split(
Expand All @@ -184,4 +184,4 @@ rule bismark_alignment_PE_2:
"../envs/environment.yaml"
threads: CORES
shell:
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} --genome {params.genome2} -1 {input.fastq1} -2 {input.fastq2} -o {params.output} --temp_dir {params.output}"
"bismark --prefix {params.prefix} --multicore {params.bismark_cores} --genome {params.genome2} -1 {input.fastq1} -2 {input.fastq2} -o {params.output} --temp_dir {params.output} 2> {log}"
24 changes: 12 additions & 12 deletions rules/build_eagle.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -44,11 +44,11 @@ rule download_eagle:
params:
eagle_version=EAGLE_VERSION,
log:
"logs/download_eagle.log",
f"{OUTPUT_DIR}logs/download_eagle.log",
conda:
ENV_PATH
shell:
"wget https://github.com/tony-kuo/eagle/archive/v{params.eagle_version}.tar.gz -O {output.eagle_tar}"
"wget https://github.com/tony-kuo/eagle/archive/v{params.eagle_version}.tar.gz -O {output.eagle_tar} 2> {log}"


rule extract_eagle:
Expand All @@ -59,11 +59,11 @@ rule extract_eagle:
params:
build_prefix=lambda w, input: os.path.split(input.eagle_tar)[0],
log:
"logs/extract_eagle.log",
f"{OUTPUT_DIR}logs/extract_eagle.log",
conda:
ENV_PATH
shell:
"tar -C {params.build_prefix} -vxf {input.eagle_tar}"
"tar -C {params.build_prefix} -vxf {input.eagle_tar} 2> {log}"


rule download_htslib:
Expand All @@ -73,11 +73,11 @@ rule download_htslib:
htslib_version=HTSLIB_VERSION,
htslib_tar_name=HTSLIB_TAR_NAME,
log:
"logs/download_htslib.log",
f"{OUTPUT_DIR}logs/download_htslib.log",
conda:
ENV_PATH
shell:
"wget https://github.com/samtools/htslib/releases/download/{params.htslib_version}/{params.htslib_tar_name} -O {output.htslib_tar}"
"wget https://github.com/samtools/htslib/releases/download/{params.htslib_version}/{params.htslib_tar_name} -O {output.htslib_tar} 2> {log}"


rule extract_htslib:
Expand All @@ -88,11 +88,11 @@ rule extract_htslib:
params:
build_prefix=lambda w, input: os.path.split(input.htslib_tar)[0],
log:
"logs/extract_htslib.log",
f"{OUTPUT_DIR}logs/extract_htslib.log",
conda:
ENV_PATH
shell:
"tar -C {params.build_prefix} -vxf {input.htslib_tar}"
"tar -C {params.build_prefix} -vxf {input.htslib_tar} 2> {log}"


rule build_eagle:
Expand All @@ -106,12 +106,12 @@ rule build_eagle:
eagle_dir_path=lambda w, input: os.path.split(input.eagle_mk)[0],
eagle_mk_flags=EAGLE_MK_FLAGS,
log:
"logs/build_eagle.log",
f"{OUTPUT_DIR}logs/build_eagle.log",
conda:
ENV_PATH
threads: CORES
shell:
"{params.eagle_mk_env} make -j {threads} -C {params.eagle_dir_path} {params.eagle_mk_flags}"
"{params.eagle_mk_env} make -j {threads} -C {params.eagle_dir_path} {params.eagle_mk_flags} 2> {log}"


rule install_eagle:
Expand All @@ -124,8 +124,8 @@ rule install_eagle:
eagle_dir_path=lambda w, input: os.path.split(input.eagle_bin)[0],
eagle_mk_flags=EAGLE_MK_FLAGS,
log:
"logs/install_eagle.log",
f"{OUTPUT_DIR}logs/install_eagle.log",
conda:
ENV_PATH
shell:
"{params.eagle_mk_env} make -C {params.eagle_dir_path} install {params.eagle_mk_flags}"
"{params.eagle_mk_env} make -C {params.eagle_dir_path} install {params.eagle_mk_flags} 2> {log}"
8 changes: 4 additions & 4 deletions rules/deduplication.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,15 @@ rule deduplication_SE:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/deduplication/{{sample}}_{{one_or_two}}/{{one_or_two}}.{{sample}}_bismark_bt2.deduplicated.bam",
log:
f"logs/deduplication_{{sample}}_{{one_or_two}}_SE.log",
f"{OUTPUT_DIR}logs/deduplication_{{sample}}_{{one_or_two}}_SE.log",
params:
f"{OUTPUT_DIR}Bismark/deduplication/{{sample}}_{{one_or_two}}/",
benchmark:
f"{OUTPUT_DIR}benchmark/dedup_se{{one_or_two}}_{{sample}}.txt"
conda:
"../envs/environment.yaml"
shell:
"deduplicate_bismark -s --output_dir {params} --bam {input}"
"deduplicate_bismark -s --output_dir {params} --bam {input} 2> {log}"


## Run deduplication of the alignments to remove duplicated reads for PE reads (GENOME_PARENT_1)
Expand All @@ -42,12 +42,12 @@ rule deduplication_PE:
if config["RUN_TRIMMING"]
else f"{OUTPUT_DIR}Bismark/deduplication/{{sample}}_{{one_or_two}}/{{one_or_two}}.{{sample}}_{str(config['PAIR_1'])}_bismark_bt2_pe.deduplicated.bam",
log:
f"logs/deduplication_{{sample}}_{{one_or_two}}_PE.log",
f"{OUTPUT_DIR}logs/deduplication_{{sample}}_{{one_or_two}}_PE.log",
params:
f"{OUTPUT_DIR}Bismark/deduplication/{{sample}}_{{one_or_two}}/",
benchmark:
f"{OUTPUT_DIR}benchmark/dedup_pe{{one_or_two}}_{{sample}}.txt"
conda:
"../envs/environment.yaml"
shell:
"deduplicate_bismark -p --output_dir {params} --bam {input}"
"deduplicate_bismark -p --output_dir {params} --bam {input} 2> {log}"
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