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Keeping the linter happy
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@DrYak
DrYak committed May 27, 2024
1 parent e610d27 commit 1652c89
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Showing 5 changed files with 125 additions and 81 deletions.
18 changes: 11 additions & 7 deletions resources/auxiliary_workflows/benchmark/workflow/Snakefile
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Expand Up @@ -557,15 +557,19 @@ rule bed_file_single_amplicon:
rule run_method_local:
input:
script=srcdir("../resources/method_definitions/{method}.py"),
fname_bam=lambda wildcards: f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reads.{{seq_mode}}.bam"
if wildcards.seq_mode == "amplicon"
else f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reads.{{seq_mode}}.bam",
fname_bam=lambda wildcards: (
f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reads.{{seq_mode}}.bam"
if wildcards.seq_mode == "amplicon"
else f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reads.{{seq_mode}}.bam"
),
fname_bam_index=f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reads.{{seq_mode}}.bam.bai",
fname_reference=f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/reference.fasta",
fname_insert_bed=lambda wildcards: f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/scheme/reference.insert.bed"
if wildcards.seq_mode == "amplicon"
or wildcards.seq_mode_param == "single_amplicon"
else [],
fname_insert_bed=lambda wildcards: (
f"results/simulated_reads/{paramspace.wildcard_pattern}/replicates/{{replicate}}/scheme/reference.insert.bed"
if wildcards.seq_mode == "amplicon"
or wildcards.seq_mode_param == "single_amplicon"
else []
),
output:
fname_result=f"results/method_runs/{paramspace.wildcard_pattern}/{{method}}/replicates/{{replicate}}/snvs.vcf",
fname_status=touch(
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16 changes: 10 additions & 6 deletions workflow/rules/align.smk
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Expand Up @@ -13,9 +13,11 @@ rule initial_vicuna:
global_ref=reference_file,
R1="{dataset}/preprocessed_data/R1.fastq",
R2=(
lambda wildcards: wildcards.dataset + "/preprocessed_data/R2.fastq"
if config.input["paired"]
else []
lambda wildcards: (
wildcards.dataset + "/preprocessed_data/R2.fastq"
if config.input["paired"]
else []
)
),
output:
"{dataset}/references/vicuna_consensus.fasta",
Expand Down Expand Up @@ -667,9 +669,11 @@ elif config.general["aligner"] == "minimap":
SEED="--seed 42",
EXTRA=config.minimap_align["extra"],
PRESET=config.minimap_align["preset"],
SECONDARY="--secondary=yes --secondary-seq"
if config.minimap_align["secondary"]
else "--secondary=no",
SECONDARY=(
"--secondary=yes --secondary-seq"
if config.minimap_align["secondary"]
else "--secondary=no"
),
FILTER="-f 2" if config.input["paired"] else "-F 4",
MINIMAP=config.applications["minimap"],
SAMTOOLS=config.applications["samtools"],
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40 changes: 25 additions & 15 deletions workflow/rules/dehuman.smk
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Expand Up @@ -10,9 +10,11 @@ rule dh_reuse_alignreject:
# this rule re-use the rejected reads in align.smk (e.g. ngshmmalign's /alignments/rejects.sam)
# (useful when in parallel with the main processing)
input:
reject_aln=rules.hmm_align.output.reject_aln
if config["general"]["aligner"] == "ngshmmalign"
else temp_prefix("{dataset}/alignments/tmp_aln.sam"),
reject_aln=(
rules.hmm_align.output.reject_aln
if config["general"]["aligner"] == "ngshmmalign"
else temp_prefix("{dataset}/alignments/tmp_aln.sam")
),
output:
reject_1=temp_with_prefix("{dataset}/alignments/reject_R1.fastq.gz"),
reject_2=temp_with_prefix("{dataset}/alignments/reject_R2.fastq.gz"),
Expand Down Expand Up @@ -115,12 +117,16 @@ rule dh_hostalign:
input:
host_ref=config.dehuman["ref_host"],
ref_index=multiext(config.dehuman["ref_host"], *bwa_idx_ext),
reject_1=rules.dh_redo_alignreject.output.reject_1
if config["dehuman"]["catchup"]
else rules.dh_reuse_alignreject.output.reject_1,
reject_2=rules.dh_redo_alignreject.output.reject_2
if config["dehuman"]["catchup"]
else rules.dh_reuse_alignreject.output.reject_2,
reject_1=(
rules.dh_redo_alignreject.output.reject_1
if config["dehuman"]["catchup"]
else rules.dh_reuse_alignreject.output.reject_1
),
reject_2=(
rules.dh_redo_alignreject.output.reject_2
if config["dehuman"]["catchup"]
else rules.dh_reuse_alignreject.output.reject_2
),
output:
host_aln=temp_with_prefix("{dataset}/alignments/host_aln.sam"),
params:
Expand Down Expand Up @@ -157,12 +163,16 @@ rule dh_hostalign:
rule dh_filter:
input:
host_aln=temp_prefix("{dataset}/alignments/host_aln.sam"),
R1=partial(raw_data_file, pair=1)
if config["dehuman"]["catchup"]
else temp_prefix("{dataset}/extracted_data/R1.fastq"),
R2=partial(raw_data_file, pair=2)
if config["dehuman"]["catchup"]
else temp_prefix("{dataset}/extracted_data/R2.fastq"),
R1=(
partial(raw_data_file, pair=1)
if config["dehuman"]["catchup"]
else temp_prefix("{dataset}/extracted_data/R1.fastq")
),
R2=(
partial(raw_data_file, pair=2)
if config["dehuman"]["catchup"]
else temp_prefix("{dataset}/extracted_data/R2.fastq")
),
output:
filter_count="{dataset}/alignments/dehuman.count",
filter_list=temp_with_prefix("{dataset}/alignments/dehuman.filter"),
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54 changes: 31 additions & 23 deletions workflow/rules/publish.smk
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Expand Up @@ -16,35 +16,43 @@ rule prepare_upload:
input:
R1=partial(raw_data_file, pair=1) if config.upload["orig_fastq"] else [],
R2=partial(raw_data_file, pair=2) if config.upload["orig_fastq"] else [],
orig_cram=[
"{dataset}/raw_uploads/raw_reads.cram",
"{dataset}/raw_uploads/raw_reads.cram.%s" % config.general["checksum"],
]
if config.upload["orig_cram"]
else [],
dehuman=[
"{dataset}/raw_uploads/dehuman.cram",
"{dataset}/raw_uploads/dehuman.cram.%s" % config.general["checksum"],
]
if config.output["dehumanized_raw_reads"]
else [],
orig_cram=(
[
"{dataset}/raw_uploads/raw_reads.cram",
"{dataset}/raw_uploads/raw_reads.cram.%s" % config.general["checksum"],
]
if config.upload["orig_cram"]
else []
),
dehuman=(
[
"{dataset}/raw_uploads/dehuman.cram",
"{dataset}/raw_uploads/dehuman.cram.%s" % config.general["checksum"],
]
if config.output["dehumanized_raw_reads"]
else []
),
consensus_indels="{dataset}/references/consensus%s.bcftools.fasta"
% bcft_suffix(),
consensus_indels_chain="{dataset}/references/consensus%s.bcftools.chain"
% bcft_suffix(),
consensus_aligned="{dataset}/references/ref_%s_dels.fasta"
% config.upload["consensus"],
csum=[
"{dataset}/references/consensus%(suf)s.bcftools.fasta.%(csum)s"
% {"suf": bcft_suffix(), "csum": config.general["checksum"]},
"{dataset}/references/ref_majority_dels.fasta.%(csum)s"
% {"suf": bcft_suffix(), "csum": config.general["checksum"]},
]
if config.upload["checksum"]
else [],
frameshift_deletions_check="{dataset}/references/frameshift_deletions_check.tsv"
if config.output["QA"]
else [],
csum=(
[
"{dataset}/references/consensus%(suf)s.bcftools.fasta.%(csum)s"
% {"suf": bcft_suffix(), "csum": config.general["checksum"]},
"{dataset}/references/ref_majority_dels.fasta.%(csum)s"
% {"suf": bcft_suffix(), "csum": config.general["checksum"]},
]
if config.upload["checksum"]
else []
),
frameshift_deletions_check=(
"{dataset}/references/frameshift_deletions_check.tsv"
if config.output["QA"]
else []
),
output:
upload_prepared_touch="{dataset}/upload_prepared.touch",
params:
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78 changes: 48 additions & 30 deletions workflow/rules/signatures.smk
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Expand Up @@ -61,9 +61,11 @@ rule cooc:
COJAC=config.applications["cojac"],
name=ID,
sep=config.general["id_separator"],
out_format="--multiindex"
if config.cooc["out_format"] == "columns"
else "--multiindex --lines",
out_format=(
"--multiindex"
if config.cooc["out_format"] == "columns"
else "--multiindex --lines"
),
log:
outfile="{dataset}/signatures/cooc.out.log",
errfile="{dataset}/signatures/cooc.err.log",
Expand Down Expand Up @@ -104,9 +106,11 @@ rule cohort_cooc:
params:
COJAC=config.applications["cojac"],
sep=config.general["id_separator"],
out_format="--multiindex"
if config.cooc["out_format"] == "columns"
else "--multiindex --lines",
out_format=(
"--multiindex"
if config.cooc["out_format"] == "columns"
else "--multiindex --lines"
),
log:
outfile=cohortdir("cohort_cooc.{proto}.out.log"),
errfile=cohortdir("cohort_cooc.{proto}.err.log"),
Expand Down Expand Up @@ -222,26 +226,36 @@ if config.timeline["local"]:
rule timeline:
input:
samples_tsv=config.input["samples_file"],
locations=config.timeline["locations_table"]
if config.timeline["locations_table"]
else [],
locations=(
config.timeline["locations_table"]
if config.timeline["locations_table"]
else []
),
regex=config.timeline["regex_yaml"] if config.timeline["regex_yaml"] else [],
output:
timeline=cohortdir("timeline.tsv"),
locations_list=cohortdir("locations_list.yaml")
if config.timeline["locations_table"]
else [],
locations_list=(
cohortdir("locations_list.yaml")
if config.timeline["locations_table"]
else []
),
params:
maketimeline=cachepath(config.timeline["script"], executable=True),
locations=f"--locations {config.timeline['locations_table']}"
if config.timeline["locations_table"]
else "",
regex=f"--regex-config {config.timeline['regex_yaml']}"
if config.timeline["regex_yaml"]
else "",
out_locations=f"--out-locations {cohortdir('locations_list.yaml')}"
if config.timeline["locations_table"] or config.timeline["regex_yaml"]
else "",
locations=(
f"--locations {config.timeline['locations_table']}"
if config.timeline["locations_table"]
else ""
),
regex=(
f"--regex-config {config.timeline['regex_yaml']}"
if config.timeline["regex_yaml"]
else ""
),
out_locations=(
f"--out-locations {cohortdir('locations_list.yaml')}"
if config.timeline["locations_table"] or config.timeline["regex_yaml"]
else ""
),
options=config.timeline["options"],
log:
outfile=cohortdir("timeline.out.log"),
Expand Down Expand Up @@ -296,20 +310,24 @@ rule deconvolution:
input:
tallymut=cohortdir("tallymut.tsv.zst"),
deconv_conf=config.deconvolution["deconvolution_config"],
var_conf=config.deconvolution["variants_config"]
if config.deconvolution["variants_config"]
else cohortdir("variants_pangolin.yaml"),
var_dates=config.deconvolution["variants_dates"]
if config.deconvolution["variants_dates"]
else [],
var_conf=(
config.deconvolution["variants_config"]
if config.deconvolution["variants_config"]
else cohortdir("variants_pangolin.yaml")
),
var_dates=(
config.deconvolution["variants_dates"]
if config.deconvolution["variants_dates"]
else []
),
output:
deconvoluted=cohortdir("deconvoluted.tsv.zst"),
deconv_json=cohortdir("deconvoluted_upload.json"),
params:
LOLLIPOP=config.applications["lollipop"],
out_format="--fmt-columns"
if config.deconvolution["out_format"] == "columns"
else "",
out_format=(
"--fmt-columns" if config.deconvolution["out_format"] == "columns" else ""
),
seed="--seed=42",
log:
outfile=cohortdir("deconvoluted.out.log"),
Expand Down

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