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Add benchmark directive to each rule #228

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Add benchmark directive to each rule #228

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1e80e02
add benchmark directive to each rule
bluegenes May 1, 2021
e782aad
rm comment about benchmarks not being used
bluegenes May 1, 2021
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35 changes: 35 additions & 0 deletions dammit/workflows/annotate.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@ rule dammit_rename_transcriptome:
names=os.path.join(results_dir, "{transcriptome}.namemap.csv")
log:
os.path.join(logs_dir, "{transcriptome}.rename.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.rename.benchmark")
threads: 1
params:
basename = config.get("basename", None),
Expand All @@ -36,6 +38,8 @@ rule dammit_transcriptome_stats:
per_transcript_fn = os.path.join(results_dir, '{transcriptome}.per-transcript-stats.csv')
log:
os.path.join(logs_dir, '{transcriptome}.stats.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.stats.benchmark')
threads: 1
shell:
"""
Expand All @@ -54,6 +58,8 @@ rule transdecoder_longorfs:
os.path.join(results_dir, '{transcriptome}.transdecoder_dir/longest_orfs.pep')
log:
os.path.join(logs_dir, '{transcriptome}.transdecoder-longorfs.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.transdecoder-longorfs.benchmark')
params:
extra = config['transdecoder_longorfs']['params'].get('extra', '-m 80 ')
threads: 1
Expand All @@ -75,6 +81,8 @@ rule hmmscan:
domtblout = os.path.join(results_dir,'{transcriptome}.x.Pfam-A.hmmscan-domtbl.txt') # save parseable table of per-domain hits to file <f>
log:
os.path.join(logs_dir, '{transcriptome}.x.Pfam-A.hmmscan.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.x.Pfam-A.hmmscan.benchmark')
params:
evalue_threshold = GLOBAL_EVALUE if GLOBAL_EVALUE is not None else config['hmmscan']['params'].get("evalue", 0.00001),
extra = config['hmmscan']['params'].get('extra', ''),
Expand All @@ -99,6 +107,8 @@ rule transdecoder_predict:
os.path.join(results_dir, '{transcriptome}.fasta.transdecoder.gff3')
log:
os.path.join(logs_dir, '{transcriptome}.transdecoder-predict.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.transdecoder-predict.benchmark')
params:
extra= config['transdecoder_predict']['params'].get('extra', '')
threads: 1
Expand All @@ -119,6 +129,8 @@ rule hmmer_remap:
os.path.join(results_dir, '{transcriptome}.x.{database}.remapped.csv')
log:
os.path.join(logs_dir, '{transcriptome}.x.{database}.hmmer_remap.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.x.{database}.hmmer_remap.benchmark')
threads: 1
shell:
"""
Expand All @@ -142,6 +154,8 @@ rule lastal:
extra = config['lastal']['params'].get('extra', ''),
log:
os.path.join(logs_dir, '{transcriptome}.x.{database}.lastal.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.x.{database}.lastal.benchmark')
threads: THREADS_PER_TASK
wrapper:
f'file://{__wrappers__}/last/lastal.wrapper.py'
Expand All @@ -164,6 +178,8 @@ rule shmlast_crbl:
extra = config['shmlast']['params'].get('extra', ''),
log:
os.path.join(logs_dir, '{transcriptome}.x.{database}.shmlast.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.x.{database}.shmlast.benchmark')
threads: THREADS_PER_TASK
wrapper: f'file://{__wrappers__}/shmlast/shmlast.wrapper.py'

Expand All @@ -181,6 +197,8 @@ rule cmscan:
tblout = os.path.join(results_dir,'{transcriptome}.x.{database}.cmscan-tblout.txt'),
log:
os.path.join(logs_dir, '{transcriptome}.x.{database}.cmscan.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.x.{database}.cmscan.benchmark')
params:
evalue_threshold = GLOBAL_EVALUE if GLOBAL_EVALUE is not None else config['cmscan']['params'].get('evalue', 0.00001),
extra = config['cmscan']['params'].get('extra', ''),
Expand All @@ -201,6 +219,8 @@ rule busco_transcripts:
os.path.join(results_dir, '{transcriptome}.busco', '{busco_db}_outputs', 'run_{busco_db}', 'full_table.tsv')
log:
os.path.join(logs_dir, "{transcriptome}.x.{busco_db}.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.x.{busco_db}.benchmark")
benchmark:
os.path.join(logs_dir, "{transcriptome}.x.{busco_db}.benchmark")
threads: THREADS_PER_TASK
Expand Down Expand Up @@ -233,6 +253,7 @@ rule plot_busco_summaries:
input: expand_busco_files
output: os.path.join(results_dir, '{transcriptome}.busco', "summary_figure.png")
log: os.path.join(logs_dir, "{transcriptome}.busco", "summary_figure.log")
benchmark: os.path.join(benchmarks_dir, "{transcriptome}.busco", "summary_figure.benchmark")
conda:
f'file://{__path__}/wrappers/busco/environment.yaml'
params:
Expand All @@ -259,6 +280,8 @@ rule dammit_busco_to_gff:
os.path.join(results_dir, '{transcriptome}.x.busco.{busco_db}.gff3')
log:
os.path.join(logs_dir, '{transcriptome}.{busco_db}.busco-to-gff3.log')
benchmark:
os.path.join(benchmarks_dir, '{transcriptome}.{busco_db}.busco-to-gff3.benchmark')
threads: 1
shell:
"""
Expand All @@ -277,6 +300,8 @@ rule dammit_cmscan_to_gff:
os.path.join(results_dir, "{transcriptome}.x.{database}.cmscan.gff3")
log:
os.path.join(logs_dir, "{transcriptome}.x.{database}.cmscan-to-gff3.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.x.{database}.cmscan-to-gff3.benchmark")
threads: 1
shell:
"""
Expand All @@ -295,6 +320,8 @@ rule dammit_hmmscan_to_gff:
os.path.join(results_dir, "{transcriptome}.x.{database}.hmmscan.gff3")
log:
os.path.join(logs_dir, "{transcriptome}.x.{database}.hmmscan-to-gff3.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.x.{database}.hmmscan-to-gff3.benchmark")
threads: 1
shell:
"""
Expand Down Expand Up @@ -331,6 +358,8 @@ rule dammit_maf_to_gff:
os.path.join(results_dir, "{transcriptome}.x.{database}.lastal.gff3")
log:
os.path.join(logs_dir, "{transcriptome}.x.{database}.lastal.maf-to-gff3.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.x.{database}.lastal.maf-to-gff3.benchmark")
threads: 1
shell:
"""
Expand All @@ -348,6 +377,8 @@ rule dammit_shmlast_to_gff:
os.path.join(results_dir, "{transcriptome}.x.{database}.shmlast_crbl.gff3")
log:
os.path.join(logs_dir, "{transcriptome}.x.{database}.shmlast-to-gff3.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.x.{database}.shmlast-to-gff3.benchmark")
threads: 1
shell:
"""
Expand All @@ -364,6 +395,8 @@ rule dammit_merge_gff:
os.path.join(results_dir, "{transcriptome}.dammit.gff3"),
log:
os.path.join(logs_dir, "{transcriptome}.merge_gffs.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.merge_gffs.benchmark")
threads: 1
shell:
"""
Expand All @@ -383,6 +416,8 @@ rule dammit_annotate_fasta:
os.path.join(results_dir, "{transcriptome}.dammit.fasta")
log:
os.path.join(logs_dir, "{transcriptome}.annotate_fasta.log")
benchmark:
os.path.join(benchmarks_dir, "{transcriptome}.annotate_fasta.benchmark")
params:
name_map = '' if config['rename'] else '--name-map ' + rules.dammit_rename_transcriptome.output.names
threads: 1
Expand Down
1 change: 0 additions & 1 deletion dammit/workflows/dammit.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ results_dir = config["output_dir"]
logs = config.get("logs_dir", "logs")
logs_dir = os.path.join(results_dir, logs)

# Benchmarks aren't run for now, but we could easily turn them on
benchmarks = config.get("benchmark_dir", "benchmarks")
benchmarks_dir = os.path.join(results_dir, benchmarks)

Expand Down
13 changes: 10 additions & 3 deletions dammit/workflows/databases.snakefile
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Expand Up @@ -18,6 +18,7 @@ rule download_and_gunzip:
fileformat = lambda wildcards: DATABASES[wildcards.database].get('fileformat', False),
folder = lambda wildcards: DATABASES[wildcards.database].get('folder', False)
log: os.path.join(logs_dir, '{database}.{file_type}.log')
benchmark: os.path.join(benchmarks_dir, '{database}.{file_type}.benchmark')
wildcard_constraints:
file_type = "hmm|cm|fasta|txt|ini|done"
threads: 1
Expand All @@ -39,7 +40,9 @@ rule lastdb:
wildcard_constraints:
file_type = "fasta|txt"
log:
os.path.join(results_dir, "{database}.{file_type}_lastdb.log")
os.path.join(logs_dir, "{database}.{file_type}_lastdb.log")
benchmark:
os.path.join(benchmarks_dir, "{database}.{file_type}_lastdb.benchmark")
threads: THREADS_PER_TASK
wrapper: f"file://{__wrappers__}/last/lastdb.wrapper.py"

Expand All @@ -58,7 +61,9 @@ rule hmmpress:
os.path.join(config["database_dir"], "{database}.hmm.h3m"),
os.path.join(config["database_dir"], "{database}.hmm.h3p")
log:
os.path.join(results_dir, "{database}_hmmpress.log")
os.path.join(logs_dir, "{database}_hmmpress.log")
benchmark:
os.path.join(benchmarks_dir, "{database}_hmmpress.benchmark")
params:
extra=config["hmmpress"]["params"].get("extra", ""),
threads: 1
Expand All @@ -78,7 +83,9 @@ rule infernal_cmpress:
os.path.join(config["database_dir"],"{database}.cm.i1m"),
os.path.join(config["database_dir"],"{database}.cm.i1p")
log:
os.path.join(results_dir, "cmpress_{database}.log")
os.path.join(logs_dir, "cmpress_{database}.log")
benchmark:
os.path.join(benchmarks_dir, "cmpress_{database}.benchmark")
params:
extra=config["cmpress"]["params"].get("extra", ""),
threads: 1
Expand Down