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ahmigahmig
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replace logs directory variable with pathvars
1 parent e45863a commit c752e29

12 files changed

Lines changed: 68 additions & 73 deletions

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‎workflow/core.smk‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,5 @@
1-
BASE_PATH = Path(workflow.basedir).parent.resolve()
2-
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include: "rules/common.smk"
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5-
# Logging
6-
LOGDIR = Path("<results>/<logs>")
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# Report
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REPORT_DIR_PLOTS = Path("<results>/<dataset>/report/plots")
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REPORT_DIR_TABLES = Path("<results>/<dataset>/report/tables")

‎workflow/rules/asr.smk‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ rule reconstruct_ancestral_sequence:
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folder = directory("<results>/<dataset>/tree"),
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state_file = "<results>/<dataset>/tree/asr.state"
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log:
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LOGDIR / "reconstruct_ancestral_sequence" / "log.txt"
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"<logs>/<dataset>/reconstruct_ancestral_sequence/log.txt"
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shell:
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"mkdir -p {output.folder} && "
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"iqtree2 -seed {params.seed} "
@@ -33,6 +33,6 @@ rule ancestor_fasta:
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output:
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fasta = report("<results>/<dataset>/ancestor.fasta")
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log:
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LOGDIR / "ancestor_fasta" / "log.txt"
36+
"<logs>/<dataset>/ancestor_fasta/log.txt"
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script:
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"../scripts/ancestor_fasta.py"

‎workflow/rules/context.smk‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ rule download_context:
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metadata = temp("<results>/<dataset>/context/metadata.csv"),
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duplicate_accids = "<results>/<dataset>/context/duplicate_accession_ids.txt",
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log:
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LOGDIR / "download_context" / "log.txt"
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"<logs>/<dataset>/download_context/log.txt"
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retries: 2
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script:
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"../scripts/download_context.R"
@@ -46,7 +46,7 @@ rule align_context:
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folder = directory("<results>/<dataset>/context/nextalign"),
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fasta = "<results>/<dataset>/context/nextalign/context_sequences.aligned.fasta"
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log:
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LOGDIR / "align_context" / "log.txt"
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"<logs>/<dataset>/align_context/log.txt"
5050
shell:
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"nextalign run -j {threads} -O {output.folder} -o {output.fasta} -n {params.name} --include-reference -r {input.ref_fasta} {input.fasta} >{log} 2>&1"
5252

@@ -65,7 +65,7 @@ rule mask_context:
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output:
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fasta = "<results>/<dataset>/context/nextalign/context_sequences.aligned.masked.fasta"
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log:
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LOGDIR / "mask_context" / "log.txt"
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"<logs>/<dataset>/mask_context/log.txt"
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script:
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"../scripts/mask_aln.py"
7171

@@ -89,7 +89,7 @@ rule ml_context_tree:
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folder = directory("<results>/<dataset>/tree_context"),
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ml = "<results>/<dataset>/tree_context/context.treefile"
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log:
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LOGDIR / "ml_context_tree" / "log.txt"
92+
"<logs>/<dataset>/ml_context_tree/log.txt"
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shell:
9494
"exec >{log} && exec 2>&1; "
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"awk '/^>/{{p=seen[$0]++}}!p' {input.fasta} {input.outgroup_aln} >aln.fasta && "

‎workflow/rules/demix.smk‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ rule demix_barcode_update:
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pathogens = "<results>/<dataset>/demixing/freyja_data/pathogen_config.yml",
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usher_barcodes = "<results>/<dataset>/demixing/freyja_data/usher_barcodes.feather"
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log:
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LOGDIR / "demix_barcode_update" / "log.txt"
17+
"<logs>/<dataset>/demix_barcode_update/log.txt"
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shell:
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"mkdir -p {output.folder:q} && "
2020
"freyja update --outdir {output.folder:q} --pathogen {params.pathogen:q} >{log} 2>&1"
@@ -34,8 +34,8 @@ rule demix_preprocessing:
3434
depth_file = "<results>/<dataset>/demixing/{sample}/{sample}_depth.txt",
3535
variants_file = "<results>/<dataset>/demixing/{sample}/{sample}_variants.tsv",
3636
log:
37-
pileup = LOGDIR / "demix_preprocessing" / "{sample}_pileup.log.txt",
38-
ivar = LOGDIR / "demix_preprocessing" / "{sample}_ivar.log.txt",
37+
pileup = "<logs>/<dataset>/demix_preprocessing/{sample}_pileup.log.txt",
38+
ivar = "<logs>/<dataset>/demix_preprocessing/{sample}_ivar.log.txt",
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shell:
4040
"set -euo pipefail && "
4141
"samtools mpileup -aa -A -d {params.max_depth} -Q {params.minq} -q 0 -B -f {input.ref_fasta:q} {input.bam:q} >sample.pileup 2>{log.pileup:q} && "
@@ -66,7 +66,7 @@ rule demix:
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output:
6767
demix_file = "<results>/<dataset>/demixing/samples/{sample}/{sample}_demixed.tsv"
6868
log:
69-
LOGDIR / "demix" / "{sample}.log.txt"
69+
"<logs>/<dataset>/demix/{sample}.log.txt"
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shell:
7171
"freyja demix "
7272
"{input.variants_file:q} "
@@ -96,6 +96,6 @@ rule summarise_demix:
9696
output:
9797
summary_df = report("<results>/<dataset>/demixing/summary.csv")
9898
log:
99-
LOGDIR / "summarise_demix" / "log.txt"
99+
"<logs>/<dataset>/summarise_demix/log.txt"
100100
script:
101101
"../scripts/summarise_demix.R"

‎workflow/rules/distances.smk‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ rule extract_afwdist_variants:
1414
output:
1515
variants = temp("<results>/<dataset>/variants.afwdist.csv"),
1616
log:
17-
LOGDIR/"extract_afwdist_variants"/"log.txt"
17+
"<logs>/<dataset>/extract_afwdist_variants/log.txt"
1818
script:
1919
"../scripts/extract_afwdist_variants.py"
2020

@@ -29,7 +29,7 @@ rule afwdist_weighted_distances:
2929
output:
3030
distances = temp("<results>/<dataset>/distances.raw.csv"),
3131
log:
32-
LOGDIR/"afwdist_weighted_distances"/"log.txt"
32+
"<logs>/<dataset>/afwdist_weighted_distances/log.txt"
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shell:
3434
"afwdist "
3535
"-i {input.variants:q} "
@@ -47,7 +47,7 @@ rule format_afwdist_results:
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output:
4848
distances = "<results>/<dataset>/distances.csv",
4949
log:
50-
LOGDIR/"format_afwdist_results"/"log.txt"
50+
"<logs>/<dataset>/format_afwdist_results/log.txt"
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script:
5252
"../scripts/format_afwdist_results.py"
5353

@@ -62,7 +62,7 @@ rule allele_freq_tree_data:
6262
output:
6363
tree = REPORT_DIR_TABLES/"allele_freq_tree.nwk",
6464
log:
65-
LOGDIR / "allele_freq_tree_data" / "log.txt"
65+
"<logs>/<dataset>/allele_freq_tree_data/log.txt"
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script:
6767
"../scripts/report/allele_freq_tree_data.R"
6868

@@ -79,6 +79,6 @@ rule time_signal_data:
7979
table = report(REPORT_DIR_TABLES/"time_signal.csv"),
8080
json = REPORT_DIR_TABLES/"time_signal.json",
8181
log:
82-
LOGDIR / "time_signal_data" / "log.txt"
82+
"<logs>/<dataset>/time_signal_data/log.txt"
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script:
8484
"../scripts/report/time_signal_data.R"

‎workflow/rules/evolution.smk‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ rule filter_genbank_features:
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output:
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gb = "<results>/<dataset>/reference.cds.gb",
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log:
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LOGDIR / "filter_genbank_features" / "log.txt"
12+
"<logs>/<dataset>/filter_genbank_features/log.txt"
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script:
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"../scripts/filter_genbank_features.py"
1515

@@ -27,7 +27,7 @@ rule n_s_sites:
2727
output:
2828
csv = temp("<results>/<dataset>/ancestor.n_s.sites.csv"),
2929
log:
30-
LOGDIR / "n_s_sites" / "log.txt"
30+
"<logs>/<dataset>/n_s_sites/log.txt"
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script:
3232
"../scripts/n_s_sites_from_fasta.py"
3333

@@ -42,6 +42,6 @@ rule calculate_dnds:
4242
output:
4343
table = "<results>/<dataset>/dnds.csv",
4444
log:
45-
LOGDIR / "calculate_dnds" / "log.txt"
45+
"<logs>/<dataset>/calculate_dnds/log.txt"
4646
script:
4747
"../scripts/calculate_dnds.R"

‎workflow/rules/fasta.smk‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ rule read_bam_refs:
77
output:
88
temp("<results>/<dataset>/bam_ids.txt")
99
log:
10-
LOGDIR / "read_bam_refs" / "log.txt"
10+
"<logs>/<dataset>/read_bam_refs/log.txt"
1111
shell:
1212
"""
1313
for bam_file in {input:q}; do
@@ -23,7 +23,7 @@ rule rename_fastas:
2323
output:
2424
renamed = temp("<results>/<dataset>/renamed/{sample}.fasta")
2525
log:
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LOGDIR / "rename_fastas" / "{sample}.log.txt"
26+
"<logs>/<dataset>/rename_fastas/{sample}.log.txt"
2727
shell:
2828
"sed 's/>.*/>'{wildcards.sample}'/g' {input.fasta} > {output.renamed} 2> {log}"
2929

@@ -36,7 +36,7 @@ rule concat_fasta:
3636
output:
3737
fasta = "<results>/<dataset>/sequences.fasta"
3838
log:
39-
LOGDIR / "concat_fasta" / "log.txt"
39+
"<logs>/<dataset>/concat_fasta/log.txt"
4040
shell:
4141
"cat {input} > {output.fasta} 2> {log}"
4242

@@ -52,7 +52,7 @@ rule align_fasta:
5252
folder = directory("<results>/<dataset>/nextalign"),
5353
fasta = "<results>/<dataset>/nextalign/sequences.aligned.fasta"
5454
log:
55-
LOGDIR / "align_fasta" / "log.txt"
55+
"<logs>/<dataset>/align_fasta/log.txt"
5656
shell:
5757
"nextalign run -j {threads} -O {output.folder} -o {output.fasta} -n sequences --include-reference -r {input.ref_fasta} {input.fasta} >{log} 2>&1"
5858

@@ -71,6 +71,6 @@ rule mask_alignment:
7171
output:
7272
fasta = "<results>/<dataset>/aligned.masked.fasta"
7373
log:
74-
LOGDIR / "mask_alignment" / "log.txt"
74+
"<logs>/<dataset>/mask_alignment/log.txt"
7575
script:
7676
"../scripts/mask_aln.py"

‎workflow/rules/fetch.smk‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ rule fetch_alignment_reference:
66
output:
77
fasta = "<results>/<dataset>/reference.fasta"
88
log:
9-
LOGDIR / "fetch_alignment_reference" / "log.txt"
9+
"<logs>/<dataset>/fetch_alignment_reference/log.txt"
1010
shell:
1111
"esearch -db nucleotide -query {params.ref} | efetch -format fasta > {output.fasta} 2> {log}"
1212

@@ -21,7 +21,7 @@ rule fetch_reference_gb:
2121
output:
2222
fasta = "<results>/<dataset>/reference.gb"
2323
log:
24-
LOGDIR / "fetch_reference_gb" / "log.txt"
24+
"<logs>/<dataset>/fetch_reference_gb/log.txt"
2525
shell:
2626
"esearch -db {params.database} -query {params.ref} | efetch -format {params.format} > {output.fasta} 2> {log}"
2727

@@ -35,7 +35,7 @@ rule fetch_mapping_references:
3535
output:
3636
fasta = select_mapping_references_fasta()
3737
log:
38-
LOGDIR / "fetch_mapping_references" / "log.txt"
38+
"<logs>/<dataset>/fetch_mapping_references/log.txt"
3939
shell:
4040
"""
4141
cat {input} | while read ref_id || [[ -n $ref_id ]]; do
@@ -51,7 +51,7 @@ rule fetch_alignment_annotation:
5151
output:
5252
temp("<results>/<dataset>/reference.gff3")
5353
log:
54-
LOGDIR / "fetch_alignment_annotation" / "log.txt"
54+
"<logs>/<dataset>/fetch_alignment_annotation/log.txt"
5555
shell:
5656
"curl 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&report=gff3&id={params.ref}' -o {output} -s 2>{log}"
5757

@@ -61,7 +61,7 @@ rule fetch_problematic_vcf:
6161
params:
6262
url = config["PROBLEMATIC_VCF"]
6363
log:
64-
LOGDIR / "fetch_problematic_vcf" / "log.txt"
64+
"<logs>/<dataset>/fetch_problematic_vcf/log.txt"
6565
output:
6666
select_problematic_vcf()
6767
shell:

‎workflow/rules/pangolin.smk‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ rule pangolin_report:
66
output:
77
report = report("<results>/<dataset>/lineage_report.csv")
88
log:
9-
LOGDIR / "pangolin_report" / "log.txt"
9+
"<logs>/<dataset>/pangolin_report/log.txt"
1010
shell:
1111
"""
1212
pangolin {input.fastas} --outfile {output.report} -t {threads} >{log} 2>&1

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