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fix: copy over spec.yaml to reduced datasets #97

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Jul 18, 2024
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fix: copy over spec.yaml to reduced datasets #97

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48 changes: 42 additions & 6 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -276,24 +276,42 @@ rule all:
f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
# -- annonars
f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
# -- mehari
f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
#
# == exomes (reduced data) directories ==================================================
#
Expand All @@ -307,24 +325,42 @@ rule all:
f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
# -- annonars
f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
# -- mehari
f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",


# ===============================================================================================
Expand Down
7 changes: 7 additions & 0 deletions rules/reduced/annonars.smk
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,10 @@ def input_subset_annonars(wildcards):
f"output/full/annonars/{wildcards.name}-{wildcards.genome_release}-"
f"{wildcards.version_multi}/rocksdb/IDENTITY"
),
"spec_yaml": (
f"output/full/annonars/{wildcards.name}-{wildcards.genome_release}-"
f"{wildcards.version_multi}/spec.yaml"
),
}
return result

Expand All @@ -27,6 +31,7 @@ rule subset_annonars: # -- create exomes subset
unpack(input_subset_annonars),
output:
rocksdb_identity="output/reduced-{set_name}/annonars/{name}-{genome_release}-{version_multi}/rocksdb/IDENTITY",
spec_yaml="output/reduced-{set_name}/annonars/{name}-{genome_release}-{version_multi}/spec.yaml",
wildcard_constraints:
name=RE_NAME,
genome_release=RE_GENOME,
Expand All @@ -44,4 +49,6 @@ rule subset_annonars: # -- create exomes subset
--path-in $(dirname {input.rocksdb_identity}) \
--path-out $(dirname {output.rocksdb_identity}) \
--path-beds {input.bed}

cp {input.spec_yaml} {output.spec_yaml}
"""
7 changes: 7 additions & 0 deletions rules/reduced/mehari.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,10 @@ def input_subset_mehari(wildcards):
f"output/full/mehari/freqs-{wildcards.genome_release}-"
f"{wildcards.version_multi}/rocksdb/IDENTITY"
),
"spec_yaml": (
f"output/full/mehari/freqs-{wildcards.genome_release}-"
f"{wildcards.version_multi}/spec.yaml"
),
}
return result

Expand All @@ -27,6 +31,7 @@ rule subset_mehari: # -- create exomes subset
unpack(input_subset_mehari),
output:
rocksdb_identity="output/reduced-{set_name}/mehari/freqs-{genome_release}-{version_multi}/rocksdb/IDENTITY",
spec_yaml="output/reduced-{set_name}/mehari/freqs-{genome_release}-{version_multi}/spec.yaml",
wildcard_constraints:
genome_release=RE_GENOME,
v_hpo=RE_VERSION,
Expand All @@ -41,4 +46,6 @@ rule subset_mehari: # -- create exomes subset
--path-in $(dirname {input.rocksdb_identity}) \
--path-out $(dirname {output.rocksdb_identity}) \
--path-beds {input.bed}

cp {input.spec_yaml} {output.spec_yaml}
"""
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