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feat: write manifest files to output (#92) (#99)
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* feat: write manifest files to output (#92)

* wi

* wip
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@holtgrewe
holtgrewe authored Jul 22, 2024
1 parent da6c54c commit 5627632
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1 change: 1 addition & 0 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ dependencies:
- attrs
- cattrs
- click
- hashdeep
- loguru
- numpy
- pydantic
Expand Down
12 changes: 12 additions & 0 deletions rules/output/annonars/alphamissense.smk
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Expand Up @@ -20,6 +20,9 @@ rule output_annonars_alphamissense: # -- build AlphaMissense RocksDB with annon
spec_yaml=(
"output/full/annonars/alphamissense-{genome_release}-{v_alphamissense}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/alphamissense-{genome_release}-{v_alphamissense}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -58,4 +61,13 @@ rule output_annonars_alphamissense: # -- build AlphaMissense RocksDB with annon
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
10 changes: 10 additions & 0 deletions rules/output/annonars/cadd.smk
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Expand Up @@ -53,6 +53,7 @@ rule output_annonars_cadd: # -- build CADD RocksDB with annonars
"output/full/annonars/cadd-{genome_release}-{v_cadd}+{v_annonars}/rocksdb/IDENTITY"
),
spec_yaml=("output/full/annonars/cadd-{genome_release}-{v_cadd}+{v_annonars}/spec.yaml"),
manifest=("output/full/annonars/cadd-{genome_release}-{v_cadd}+{v_annonars}/MANIFEST.txt"),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -93,4 +94,13 @@ rule output_annonars_cadd: # -- build CADD RocksDB with annonars
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
10 changes: 10 additions & 0 deletions rules/output/annonars/cons.smk
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Expand Up @@ -11,6 +11,7 @@ rule output_annonars_cons: # -- build UCSC conservation track RocksDB with anno
"output/full/annonars/cons-{genome_release}-{v_cons}+{v_annonars}/rocksdb/IDENTITY"
),
spec_yaml=("output/full/annonars/cons-{genome_release}-{v_cons}+{v_annonars}/spec.yaml"),
manifest=("output/full/annonars/cons-{genome_release}-{v_cons}+{v_annonars}/MANIFEST.txt"),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand All @@ -37,4 +38,13 @@ rule output_annonars_cons: # -- build UCSC conservation track RocksDB with anno
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/dbnsfp.smk
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Expand Up @@ -16,6 +16,9 @@ rule output_annonars_dbnsfp: # -- build dbNSFP RocksDB with annonars
"output/full/annonars/dbnsfp-{genome_release}-{v_dbnsfp}+{v_annonars}/rocksdb/IDENTITY"
),
spec_yaml=("output/full/annonars/dbnsfp-{genome_release}-{v_dbnsfp}+{v_annonars}/spec.yaml"),
manifest=(
"output/full/annonars/dbnsfp-{genome_release}-{v_dbnsfp}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -59,4 +62,13 @@ rule output_annonars_dbnsfp: # -- build dbNSFP RocksDB with annonars
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/dbscsnv.smk
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Expand Up @@ -18,6 +18,9 @@ rule output_annonars_dbscsnv: # -- build dbscSNV RocksDB with annonars
spec_yaml=(
"output/full/annonars/dbscsnv-{genome_release}-{v_dbscsnv}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/dbscsnv-{genome_release}-{v_dbscsnv}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -61,4 +64,13 @@ rule output_annonars_dbscsnv: # -- build dbscSNV RocksDB with annonars
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
10 changes: 10 additions & 0 deletions rules/output/annonars/dbsnp.smk
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Expand Up @@ -11,6 +11,7 @@ rule output_annonars_dbsnp: # -- build dbSNP RocksDB with annonars
"output/full/annonars/dbsnp-{genome_release}-{v_dbsnp}+{v_annonars}/rocksdb/IDENTITY"
),
spec_yaml=("output/full/annonars/dbsnp-{genome_release}-{v_dbsnp}+{v_annonars}/spec.yaml"),
manifest=("output/full/annonars/dbsnp-{genome_release}-{v_dbsnp}+{v_annonars}/MANIFEST.txt"),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand All @@ -37,4 +38,13 @@ rule output_annonars_dbsnp: # -- build dbSNP RocksDB with annonars
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/functional.smk
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Expand Up @@ -39,6 +39,9 @@ rule output_annonars_functional: # -- build annonars functional RocksDB file
spec_yaml=(
"output/full/annonars/functional-{genome_release}-{v_refseq}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/functional-{genome_release}-{v_refseq}+{v_annonars}/MANIFEST.txt"
),
wildcard_constraints:
v_refseq=RE_VERSION,
v_annonars=RE_VERSION,
Expand All @@ -64,4 +67,13 @@ rule output_annonars_functional: # -- build annonars functional RocksDB file
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
13 changes: 13 additions & 0 deletions rules/output/annonars/genes.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,10 @@ rule output_annonars_genes: # -- build annonars genes RocksDB file
"output/full/annonars/genes-{v_acmg_sf}+{v_gnomad_constraints}+{v_dbnsfp}+{v_hpo}+{date}+{v_annonars}/"
"spec.yaml"
),
manifest=(
"output/full/annonars/genes-{v_acmg_sf}+{v_gnomad_constraints}+{v_dbnsfp}+{v_hpo}+{date}+{v_annonars}/"
"MANIFEST.txt"
),
wildcard_constraints:
v_acmg_sf=RE_VERSION,
v_gnomad_constraints=RE_VERSION,
Expand Down Expand Up @@ -73,4 +77,13 @@ rule output_annonars_genes: # -- build annonars genes RocksDB file
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/gnomad_exomes.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ rule output_annonars_gnomad_exomes: # -- build gnomAD-exomes RocksDB with annon
spec_yaml=(
"output/full/annonars/gnomad-exomes-{genome_release}-{v_gnomad}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/gnomad-exomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -55,4 +58,13 @@ rule output_annonars_gnomad_exomes: # -- build gnomAD-exomes RocksDB with annon
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/gnomad_genomes.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ rule output_annonars_gnomad_genomes: # -- build gnomAD-genomes RocksDB with ann
spec_yaml=(
"output/full/annonars/gnomad-genomes-{genome_release}-{v_gnomad}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/gnomad-genomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -55,4 +58,13 @@ rule output_annonars_gnomad_genomes: # -- build gnomAD-genomes RocksDB with ann
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/gnomad_mtdna.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ rule output_annonars_gnomad_mtdna: # -- build gnomAD-mtDNA RocksDB with annonar
spec_yaml=(
"output/full/annonars/gnomad-mtdna-{genome_release}-{v_gnomad}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/gnomad-mtdna-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -40,4 +43,13 @@ rule output_annonars_gnomad_mtdna: # -- build gnomAD-mtDNA RocksDB with annonar
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
48 changes: 48 additions & 0 deletions rules/output/annonars/gnomad_sv.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ rule output_annonars_gnomad_sv_grch37_exac: # -- build gnomAD-SV RocksDB with a
"output/full/annonars/gnomad-sv-exomes-grch37-{v_gnomad}+{v_annonars}/rocksdb/IDENTITY",
),
spec_yaml=("output/full/annonars/gnomad-sv-exomes-grch37-{v_gnomad}+{v_annonars}/spec.yaml"),
manifest=(
"output/full/annonars/gnomad-sv-exomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -39,6 +42,15 @@ rule output_annonars_gnomad_sv_grch37_exac: # -- build gnomAD-SV RocksDB with a
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""


Expand All @@ -55,6 +67,9 @@ rule output_annonars_gnomad_sv_grch37_gnomad_sv2: # -- build gnomAD-SV RocksDB
spec_yaml=(
"output/full/annonars/gnomad-sv-genomes-grch37-{v_gnomad}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/gnomad-sv-genomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -82,6 +97,15 @@ rule output_annonars_gnomad_sv_grch37_gnomad_sv2: # -- build gnomAD-SV RocksDB
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""


Expand All @@ -96,6 +120,9 @@ rule output_annonars_gnomad_sv_grch38_gnomad_cnv4: # -- build gnomAD-SV RocksDB
"output/full/annonars/gnomad-sv-exomes-grch38-{v_gnomad}+{v_annonars}/rocksdb/IDENTITY",
),
spec_yaml=("output/full/annonars/gnomad-sv-exomes-grch38-{v_gnomad}+{v_annonars}/spec.yaml"),
manifest=(
"output/full/annonars/gnomad-sv-exomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -123,6 +150,15 @@ rule output_annonars_gnomad_sv_grch38_gnomad_cnv4: # -- build gnomAD-SV RocksDB
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""


Expand All @@ -136,6 +172,9 @@ rule output_annonars_gnomad_sv_grch38_gnomad_sv4: # -- build gnomAD-SV RocksDB
spec_yaml=(
"output/full/annonars/gnomad-sv-genomes-grch38-{v_gnomad}+{v_annonars}/spec.yaml"
),
manifest=(
"output/full/annonars/gnomad-sv-genomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand Down Expand Up @@ -164,4 +203,13 @@ rule output_annonars_gnomad_sv_grch38_gnomad_sv4: # -- build gnomAD-SV RocksDB
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
12 changes: 12 additions & 0 deletions rules/output/annonars/helix.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ rule output_annonars_helixmtdb: # -- build HelixMtDb RocksDB with annonars
spec_yaml=(
"output/full/annonars/helixmtdb-{genome_release}-{v_helixmtdb}+{v_annonars}/spec.yaml",
),
manifest=(
"output/full/annonars/helixmtdb-{genome_release}-{v_helixmtdb}+{v_annonars}/MANIFEST.txt",
),
threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
Expand All @@ -39,4 +42,13 @@ rule output_annonars_helixmtdb: # -- build HelixMtDb RocksDB with annonars
--value v_annonars={wildcards.v_annonars} \
--value v_downloader={PV.downloader} \
> {output.spec_yaml}
export TMPDIR=$(mktemp -d)
pushd $(dirname {output.spec_yaml})
rm -f MANIFEST.txt
hashdeep -l -r . >$TMPDIR/MANIFEST.txt
CHECKSUM=$(sha256sum $TMPDIR/MANIFEST.txt | cut -d ' ' -f 1)
echo "## EOF SHA256=$CHECKSUM" >> $TMPDIR/MANIFEST.txt
cp $TMPDIR/MANIFEST.txt MANIFEST.txt
popd
"""
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