diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c2096237..c5dfc33b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -80,9 +80,6 @@ jobs:
unzip qsv-0.112.0-x86_64-unknown-linux-musl.zip
cp qsv_musl-1.2.3 /usr/local/bin/qsv
- - name: Install annonars
- run: |
- sudo bash ./utils/install-annonars.sh
- name: Install python package
run: |
pip install -e .
diff --git a/Snakefile b/Snakefile
index 782ad310..f10c4408 100644
--- a/Snakefile
+++ b/Snakefile
@@ -40,6 +40,14 @@ DEV_GENE_SYMBOLS = "|".join(
# Padding to add to exons in dev and exons mode.
EXON_PADDING = 200
+GENOMEBUILDS = os.environ.get("GENOMEBUILDS", "grch37,grch38").split(",")
+
+# Define number of threads for resource-intensive tasks
+THREADS = int(os.environ.get("THREADS", "32"))
+
+# Define amount of ram for resource-intesnive tasks (in mb)
+MEMORY = int(os.environ.get("MEMORY", "196000"))
+
# ===============================================================================================
# Test Mode
# ===============================================================================================
@@ -79,20 +87,221 @@ rule help:
)
-## all -- run all rules
-rule all:
- input:
- # == work directory =====================================================================
- #
- # genes
+def generate_input_files():
+ """
+ Helper function to return the input files for the rules.
+ """
+ genomebuilds = GENOMEBUILDS
+ gnomad_versions = {
+ "grch37": DV.gnomad_v2,
+ "grch38": DV.gnomad_v4,
+ }
+ gnomad_cnv_versions = {
+ "grch37": DV.exac_cnv,
+ "grch38": DV.gnomad_cnv4,
+ }
+ gnomad_sv_versions = {
+ "grch37": DV.gnomad_sv,
+ "grch38": DV.gnomad_sv4,
+ }
+ refseq_versions = {
+ "grch37": DV.refseq_37,
+ "grch38": DV.refseq_38,
+ }
+ refseq_fe_versions = {
+ "grch37": DV.refseq_fe_37,
+ "grch38": DV.refseq_fe_38,
+ }
+ cons_versions = {
+ "grch37": DV.ucsc_cons_37,
+ "grch38": DV.ucsc_cons_38,
+ }
+ rmask_versions = {
+ "grch37": DV.ucsc_rmsk_37,
+ "grch38": DV.ucsc_rmsk_38,
+ }
+ genomic_super_dups_versions = {
+ "grch37": DV.ucsc_genomic_super_dups_37,
+ "grch38": DV.ucsc_genomic_super_dups_38,
+ }
+ lift_over_versions = {
+ "grch37": DV.ucsc_alt_seq_liftover_37,
+ "grch38": DV.ucsc_alt_seq_liftover_38,
+ }
+ lift_over_fix_versions = {
+ "grch37": DV.ucsc_fix_seq_liftover_37,
+ "grch38": DV.ucsc_fix_seq_liftover_38,
+ }
+
+ input_files = []
+ if "grch38" in genomebuilds:
+ input_files += [
+ f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv",
+ "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz",
+ f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz",
+ f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz",
+ f"work/annos/grch38/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz",
+ f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
+ f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v4}/.done",
+ f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done",
+ f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv",
+ f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz",
+ f"work/annos/grch38/features/refseq/{DV.refseq_38}/refseq_genes.bed.gz",
+ f"output/full/worker/bgdb-gnomad-exomes-cnv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-exomes-cnv-grch38.bin",
+ f"output/full/worker/bgdb-gnomad-genomes-sv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-genomes-sv-grch38.bin",
+ # ----- background/population structural variants and annotations thereof
+ f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz",
+ f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz",
+ ]
+ if "grch37" in genomebuilds:
+ input_files += [
+ f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv",
+ f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv",
+ f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz",
+ f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz",
+ f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt",
+ f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt",
+ f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1",
+ f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz",
+ f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz",
+ f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
+ f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done",
+ f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done",
+ f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv",
+ f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz",
+ f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz",
+ f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin",
+ f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin",
+ f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin",
+ f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz",
+ f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz",
+ f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz",
+ ]
+ for genomebuild in genomebuilds:
+ input_files += [
+ # -- mehari data
+ # ---- frequencies (via annonars)
+ f"output/full/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/alphamissense-{genomebuild}-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY",
+ # -- annonars data
+ # ----- sequence variant annotations
+ f"output/full/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/gnomad-mtdna-{genomebuild}-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/helixmtdb-{genomebuild}-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/gnomad-sv-exomes-{genomebuild}-{gnomad_cnv_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/gnomad-sv-genomes-{genomebuild}-{gnomad_sv_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ # ----- sequence annotation
+ f"output/full/annonars/functional-{genomebuild}-{refseq_fe_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/full/annonars/regions-{genomebuild}-{DV.today}+{PV.annonars}/rocksdb/IDENTITY",
+ # ----- conservation
+ f"output/full/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ # ----- worker
+ f"output/full/worker/masked-repeat-{genomebuild}-{rmask_versions[genomebuild]}+{PV.worker}/masked-repeat.bin",
+ f"output/full/worker/masked-segdup-{genomebuild}-{genomic_super_dups_versions[genomebuild]}+{PV.worker}/masked-segdup.bin",
+ f"output/full/worker/bgdb-dbvar-{genomebuild}-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin",
+ f"output/full/worker/bgdb-dgv-{genomebuild}-{DV.dgv}+{PV.worker}/bgdb-dgv.bin",
+ f"output/full/worker/bgdb-dgv-gs-{genomebuild}-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin",
+ f"output/full/worker/clinvar-strucvars-{genomebuild}-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin",
+ f"output/full/worker/patho-mms-{genomebuild}-{DV.patho_mms}+{PV.worker}/patho-mms.bed",
+ f"output/full/worker/tads-{genomebuild}-dixon2015/hesc.bed",
+ # -- mehari data
+ f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-ensembl-{DV.mehari_tx}.bin.zst",
+ f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-refseq-{DV.mehari_tx}.bin.zst",
+ f"output/full/mehari/genes-txs-{genomebuild}-{DV.mehari_tx}/mehari-data-txs-{genomebuild}-ensembl-and-refseq-{DV.mehari_tx}.bin.zst",
+ f"output/full/tracks/track-strucvars-dbvar-{genomebuild}-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz",
+ f"output/full/tracks/track-strucvars-dgv-{genomebuild}-{DV.dgv}+{DV.tracks}/dgv.bed.gz",
+ f"output/full/tracks/track-strucvars-dgv-gs-{genomebuild}-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz",
+ # ----- known pathogenic MMS
+ f"output/full/tracks/track-strucvars-patho-mms-{genomebuild}-{DV.patho_mms}+{DV.tracks}/patho-mms.bed",
+ # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl)
+ f"output/full/tracks/track-features-ucsc-genomicsuperdups-{genomebuild}-{genomic_super_dups_versions[genomebuild]}+{DV.tracks}/genomicSuperDups.bed.gz",
+ f"output/full/tracks/track-features-ucsc-rmsk-{genomebuild}-{rmask_versions[genomebuild]}+{DV.tracks}/rmsk.bed.gz",
+ f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-{genomebuild}-{lift_over_versions[genomebuild]}+{DV.tracks}/altSeqLiftOverPsl.bed.gz",
+ f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-{genomebuild}-{lift_over_fix_versions[genomebuild]}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz",
+ # ----- tads
+ f"output/full/tracks/track-tads-{genomebuild}-dixon2015+{DV.tracks}/hesc.bed",
+ # ----- probesets
+ f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-{genomebuild}-{DV.tracks}.bed.gz",
+ f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-{genomebuild}-{DV.tracks}.bed.gz",
+ # -- targets
+ f"output/reduced-dev/targets/{genomebuild}/refseq/{refseq_versions[genomebuild]}/refseq_target_exons.bed.gz",
+ #
+ # == development (reduced data) directories =============================================
+ #
+ # -- annonars
+ f"output/reduced-dev/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ f"output/reduced-dev/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ # -- mehari
+ f"output/reduced-dev/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-dev/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
+ #
+ # == exomes (reduced data) directories ==================================================
+ #
+ # -- targets
+ f"output/reduced-exomes/targets/{genomebuild}/refseq/{refseq_versions[genomebuild]}/refseq_target_exons.bed.gz",
+ # -- annonars
+ f"output/reduced-exomes/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/cadd-{genomebuild}-{DV.cadd}+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/cons-{genomebuild}-{cons_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/dbnsfp-{genomebuild}-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/dbscsnv-{genomebuild}-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/dbsnp-{genomebuild}-{DV.dbsnp}+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/gnomad-exomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ f"output/reduced-exomes/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/annonars/gnomad-genomes-{genomebuild}-{gnomad_versions[genomebuild]}+{PV.annonars}/spec.yaml",
+ # -- mehari
+ f"output/reduced-exomes/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+ f"output/reduced-exomes/mehari/freqs-{genomebuild}-{gnomad_versions[genomebuild]}+{gnomad_versions[genomebuild]}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
+ ]
+ # Files independent of genomebuild (or serving both)
+ input_files += [
+ # -- download
f"work/download/genes/rcnv/2022/Collins_rCNV_2022.dosage_sensitivity_scores.tsv.gz",
- "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz",
f"work/download/genes/ctd/{DV.today}/CTD_diseases.tsv.gz",
f"work/download/do/{DV.today}/omim-unmapped.csv",
+ # NB: dbNSFP is dual reference (for download)
+ # NB: dbscSNV is dual reference (for download)
+ f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz",
+ # -- genes
f"work/genes/dbnsfp/{DV.dbnsfp}/genes.tsv.gz",
"work/genes/decipher/v3/decipher_hi_prediction.tsv",
f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv",
- f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv",
f"work/genes/entrez/{DV.today}/gene_info.jsonl",
f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv",
f"work/genes/hgnc/{DV.today}/hgnc_info.jsonl",
@@ -101,266 +310,37 @@ rule all:
f"work/genes/mondo/{DV.today}/mondo.obo",
"work/genes/rcnv/2022/rcnv_collins_2022.tsv",
"work/genes/shet/2019/shet_weghorn_2019.tsv",
- f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh37.tsv",
- f"work/genes/clingen/{DV.today}/ClinGen_gene_curation_list_GRCh38.tsv",
"work/genes/domino/20190219/domino.tsv",
- # reference-specific annotations
- # -- background/population sequence variants and annotations thereof
- # ---- GRCh37
- f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz",
- f"work/download/annos/grch37/seqvars/cadd/{DV.cadd}/InDels_inclAnno.tsv.gz",
- f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}a/LICENSE.txt",
- f"work/download/annos/grch37/seqvars/dbnsfp/{DV.dbnsfp}c/LICENSE.txt",
- f"work/download/annos/grch37/seqvars/dbscsnv/{DV.dbscsnv}/dbscSNV{DV.dbscsnv}.chr1",
- f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz",
- f"work/annos/grch37/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz",
- f"work/annos/grch37/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
- f"work/download/annos/grch37/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done",
- f"work/download/annos/grch37/seqvars/gnomad_genomes/{DV.gnomad_v2}/.done",
- # ---- GRCh38
- f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/whole_genome_SNVs_inclAnno.tsv.gz",
- f"work/download/annos/grch38/seqvars/cadd/{DV.cadd}/gnomad.genomes.r3.0.indel_inclAnno.tsv.gz",
- # NB: dbNSFP is dual reference (for download)
- # NB: dbscSNV is dual reference (for download)
- f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz",
- f"work/annos/grch38/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz",
- f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
- f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v4}/.done",
- f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done",
- # -- genome browser "features" (position-specific)
- # ---- GRCh37
- f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv",
- f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz",
- f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz",
- # ---- GRCh38
- f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv",
- f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz",
- f"work/annos/grch38/features/refseq/{DV.refseq_38}/refseq_genes.bed.gz",
- #
- # == output directory ===================================================================
- #
- # -- mehari data
- # ---- frequencies (via annonars)
- f"output/full/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
- # -- annonars data
- # ----- sequence variant annotations
- f"output/full/annonars/alphamissense-grch37-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/alphamissense-grch38-{DV.alphamissense}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/helixmtdb-grch37-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/helixmtdb-grch38-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-sv-exomes-grch37-{DV.exac_cnv}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-sv-exomes-grch38-{DV.gnomad_cnv4}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-sv-genomes-grch37-{DV.gnomad_sv}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/gnomad-sv-genomes-grch38-{DV.gnomad_sv4}+{PV.annonars}/rocksdb/IDENTITY",
- # ----- sequence annotation
- f"output/full/annonars/functional-grch37-{DV.refseq_fe_37}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/functional-grch38-{DV.refseq_fe_38}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/regions-grch37-{DV.today}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/regions-grch38-{DV.today}+{PV.annonars}/rocksdb/IDENTITY",
- # ----- conservation
- f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
- f"output/full/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
- # ----- genes
+ # -- annonars
f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY",
# -- worker data
f"output/full/worker/genes-xlink-{DV.today}+{PV.worker}/genes-xlink.bin",
f"output/full/worker/acmg-sf-{DV.acmg_sf}+{PV.worker}/acmg_sf.tsv",
f"output/full/worker/mim2gene-{DV.today}+{PV.worker}/mim2gene.tsv",
- f"output/full/worker/masked-repeat-grch37-{DV.ucsc_rmsk_37}+{PV.worker}/masked-repeat.bin",
- f"output/full/worker/masked-repeat-grch38-{DV.ucsc_rmsk_38}+{PV.worker}/masked-repeat.bin",
- f"output/full/worker/masked-segdup-grch37-{DV.ucsc_genomic_super_dups_37}+{PV.worker}/masked-segdup.bin",
- f"output/full/worker/masked-segdup-grch38-{DV.ucsc_genomic_super_dups_38}+{PV.worker}/masked-segdup.bin",
- f"output/full/worker/bgdb-dbvar-grch37-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin",
- f"output/full/worker/bgdb-dbvar-grch38-{DV.dbvar}+{PV.worker}/bgdb-dbvar.bin",
- f"output/full/worker/bgdb-dgv-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv.bin",
- f"output/full/worker/bgdb-dgv-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv.bin",
- f"output/full/worker/bgdb-dgv-gs-grch37-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin",
- f"output/full/worker/bgdb-dgv-gs-grch38-{DV.dgv}+{PV.worker}/bgdb-dgv-gs.bin",
- f"output/full/worker/bgdb-gnomad-grch37-{DV.gnomad_sv}+{PV.worker}/bgdb-gnomad.bin",
- f"output/full/worker/bgdb-exac-grch37-{DV.exac_cnv}+{PV.worker}/bgdb-exac.bin",
- f"output/full/worker/bgdb-gnomad-exomes-cnv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-exomes-cnv-grch38.bin",
- f"output/full/worker/bgdb-gnomad-genomes-sv-grch38-{DV.gnomad_sv4}+{PV.worker}/bgdb-gnomad-genomes-sv-grch38.bin",
- f"output/full/worker/bgdb-g1k-grch37-{DV.g1k_svs}+{PV.worker}/bgdb-g1k.bin",
- f"output/full/worker/clinvar-strucvars-grch37-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin",
- f"output/full/worker/clinvar-strucvars-grch38-{DV.clinvar_version}+{PV.worker}/clinvar-strucvars.bin",
- f"output/full/worker/patho-mms-grch37-{DV.patho_mms}+{PV.worker}/patho-mms.bed",
- f"output/full/worker/patho-mms-grch38-{DV.patho_mms}+{PV.worker}/patho-mms.bed",
- "output/full/worker/tads-grch37-dixon2015/hesc.bed",
- "output/full/worker/tads-grch38-dixon2015/hesc.bed",
- # -- mehari data
f"output/full/mehari/genes-xlink-{DV.today}/genes-xlink.tsv",
- f"output/full/mehari/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst",
- f"output/full/mehari/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-{DV.mehari_tx}.bin.zst",
- # ----- HPO
+ # -- viguno
f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo",
f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
- # ----- background/population structural variants and annotations thereof
- f"output/full/tracks/track-strucvars-dbvar-grch37-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz",
- f"output/full/tracks/track-strucvars-dbvar-grch38-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz",
- f"output/full/tracks/track-strucvars-dgv-grch37-{DV.dgv}+{DV.tracks}/dgv.bed.gz",
- f"output/full/tracks/track-strucvars-dgv-grch38-{DV.dgv}+{DV.tracks}/dgv.bed.gz",
- f"output/full/tracks/track-strucvars-dgv-gs-grch37-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz",
- f"output/full/tracks/track-strucvars-dgv-gs-grch38-{DV.dgv_gs}+{DV.tracks}/dgv-gs.bed.gz",
- f"output/full/tracks/track-strucvars-exac-grch37-{DV.exac_cnv}+{DV.tracks}/exac.bed.gz",
- f"output/full/tracks/track-strucvars-g1k-grch37-{DV.g1k_svs}+{DV.tracks}/g1k.bed.gz",
- f"output/full/tracks/track-strucvars-gnomad-grch37-{DV.gnomad_sv}+{DV.tracks}/gnomad.bed.gz",
- f"output/full/tracks/track-strucvars-gnomad-sv-grch38-{DV.gnomad_sv4}+{DV.tracks}/gnomad-sv.bed.gz",
- f"output/full/tracks/track-strucvars-gnomad-cnv-grch38-{DV.gnomad_cnv4}+{DV.tracks}/gnomad-cnv.bed.gz",
- # ----- known pathogenic MMS
- f"output/full/tracks/track-strucvars-patho-mms-grch37-{DV.patho_mms}+{DV.tracks}/patho-mms.bed",
- f"output/full/tracks/track-strucvars-patho-mms-grch38-{DV.patho_mms}+{DV.tracks}/patho-mms.bed",
- # ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl)
- f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch37-{DV.ucsc_genomic_super_dups_37}+{DV.tracks}/genomicSuperDups.bed.gz",
- f"output/full/tracks/track-features-ucsc-genomicsuperdups-grch38-{DV.ucsc_genomic_super_dups_38}+{DV.tracks}/genomicSuperDups.bed.gz",
- f"output/full/tracks/track-features-ucsc-rmsk-grch37-{DV.ucsc_rmsk_37}+{DV.tracks}/rmsk.bed.gz",
- f"output/full/tracks/track-features-ucsc-rmsk-grch38-{DV.ucsc_rmsk_38}+{DV.tracks}/rmsk.bed.gz",
- f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch37-{DV.ucsc_alt_seq_liftover_37}+{DV.tracks}/altSeqLiftOverPsl.bed.gz",
- f"output/full/tracks/track-features-ucsc-altseqliftoverpsl-grch38-{DV.ucsc_alt_seq_liftover_38}+{DV.tracks}/altSeqLiftOverPsl.bed.gz",
- f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch37-{DV.ucsc_fix_seq_liftover_37}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz",
- f"output/full/tracks/track-features-ucsc-fixseqliftoverpsl-grch38-{DV.ucsc_fix_seq_liftover_38}+{DV.tracks}/fixSeqLiftOverPsl.bed.gz",
- # ----- tads
- f"output/full/tracks/track-tads-grch37-dixon2015+{DV.tracks}/hesc.bed",
- f"output/full/tracks/track-tads-grch38-dixon2015+{DV.tracks}/hesc.bed",
- # ----- probesets
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v4-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v5-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v6-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v7-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/agilent-all-exon-v8-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v1-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/idt-xgen-exome-research-panel-v2-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-comprehensive-exome-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-core-exome-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-exome-v2_0-grch38-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch37-{DV.tracks}.bed.gz",
- f"output/full/tracks/track-enrichment-probesets-targets/twist-refseq-exome-grch38-{DV.tracks}.bed.gz",
- #
- # == development (reduced data) directories =============================================
- #
- # -- targets
- f"output/reduced-dev/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz",
- f"output/reduced-dev/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz",
- # -- viguno
+ # -- viguno (reduced dev)
f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo",
f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
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/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-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 ==================================================
- #
- # -- targets
- f"output/reduced-exomes/targets/grch37/refseq/{DV.refseq_37}/refseq_target_exons.bed.gz",
- f"output/reduced-exomes/targets/grch38/refseq/{DV.refseq_38}/refseq_target_exons.bed.gz",
- # -- viguno
+ # -- viguno (reduced exomes)
f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo",
f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
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/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-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",
+ ]
+ return input_files
+
+
+## all -- run all rules
+rule all:
+ input:
+ generate_input_files(),
# ===============================================================================================
diff --git a/download_urls.yml b/download_urls.yml
index 1fc98681..5990fdaa 100644
--- a/download_urls.yml
+++ b/download_urls.yml
@@ -57,16 +57,17 @@
count: null
# dbNSFP v4.5a
-- url: https://dbnsfp.s3.amazonaws.com/dbNSFP4.5a.zip
+- url: https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l
excerpt_strategy:
strategy: manual
count: null
# dbNSFP v4.5c
-- url: https://dbnsfp.s3.amazonaws.com/dbNSFP4.5c.zip
+- url: https://usf.box.com/shared/static/03xsrpna0nzgrytfo2pzk326t8jad4oc
excerpt_strategy:
strategy: manual
count: null
-- url: ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbscSNV1.1.zip
+# dbscSNV v1.1
+- url: https://usf.box.com/shared/static/ffwlywsat3q5ijypvunno3rg6steqfs8
skip_upstream_check: true # does not work reliably in tests
excerpt_strategy:
strategy: manual
@@ -115,10 +116,10 @@
- url: https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz
-- url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv
-- url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv
-- url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv
-- url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
+- url: https://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv
+- url: https://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv
+- url: https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv
+- url: https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
- url: https://storage.googleapis.com/adult-gtex/annotations/v8/metadata-files/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
excerpt_strategy:
@@ -141,38 +142,63 @@
url: https://search.clinicalgenome.org/kb/reports/curation-activity-summary-report
skip_upstream_check: true # does not work reliably in tests
-- url: https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20240612/clinvar-data-extract-vars-20240612+0.17.0.tar.gz
+- url: https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20250410/clinvar-data-extract-vars-20250410+0.18.5.tar.gz
excerpt_strategy:
strategy: manual
count: null
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch37-0.4.4.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch38-0.4.4.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/hp.obo
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-refseq-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/phenotype.hpoa
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-refseq-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/phenotype_to_genes.txt
+
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-and-refseq-0.10.3.bin.zst
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-and-refseq-0.10.3.bin.zst
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
+
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch37-ensembl-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/genes_to_phenotype.txt
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.10.3/mehari-data-txs-grch38-ensembl-0.10.3.bin.zst
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: https://ftp.ensembl.org/pub/current_README
+- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/hp.obo
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
+- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/phenotype.hpoa
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
+- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/phenotype_to_genes.txt
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
+- url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2025-03-03/genes_to_phenotype.txt
+ excerpt_strategy:
+ strategy: no-excerpt
+ count: null
- comment: The UCSC listing is used for checking the versions for GRCh37.
url: https://hgdownload.cse.ucsc.edu/goldenpath/hg19/database
@@ -199,11 +225,11 @@
count: 10000
- url: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/multiz100way/alignments/knownGene.exonAA.fa.gz
-- url: http://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip
+- url: https://3dgenome.fsm.northwestern.edu/downloads/hg19.TADs.zip
excerpt_strategy:
strategy: no-excerpt
count: null
-- url: http://3dgenome.fsm.northwestern.edu/downloads/hg38.TADs.zip
+- url: https://3dgenome.fsm.northwestern.edu/downloads/hg38.TADs.zip
excerpt_strategy:
strategy: no-excerpt
count: null
@@ -250,8 +276,8 @@
strategy: head
count: 10000
-- url: 'https://ensembl.org/biomart/martservice?query='
-- url: 'https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json'
+- url: 'https://may2024.archive.ensembl.org/biomart/martservice?query='
+- url: 'https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json'
skip_upstream_check: true # does not work reliably in tests
excerpt_strategy:
strategy: manual
diff --git a/environment.yml b/environment.yml
index b8180d7d..02cfdcf3 100644
--- a/environment.yml
+++ b/environment.yml
@@ -33,23 +33,23 @@ dependencies:
- jq
# Tools for file downloads.
- aria2 >=1.36.0
- - wget
# Tool for processing BED files.
- bedops =2
# VCF/BCF/HTSlib/Samtools.
- - bcftools =1.17
- - htslib =1.17
- - samtools =1.17
+ - bcftools =1.21
+ - htslib =1.21
+ - samtools =1.21
# Parallel (de)compression.
- pigz
# Varfish related
- # - annonars =0.41.3 # current versions not on bioconda due to build issue, but docker images are available
- - viguno =0.3.1
- - mehari =0.25.5
- - varfish-server-worker =0.13.0
+ - annonars =0.44.0
+ - viguno =0.4.0
+ - mehari =0.35.1
+ - varfish-server-worker =0.17.2
# S3 uploads
- s5cmd =2.1.0
# async HTTP requests
- httpx =0.25.0
- httpcore =0.18.0
- trio
+ - qsv
diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz
deleted file mode 100644
index 3d17d229..00000000
--- a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi
deleted file mode 100644
index cb2f3577..00000000
--- a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi
+++ /dev/null
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deleted file mode 100644
index 830b58e7..00000000
--- a/excerpt-data/0106e2c5435e5972/url.txt
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diff --git a/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi b/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi
index 08c3d4de..5979c3e4 100644
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+++ b/excerpt-data/02b0e15df1b90b86/gnomad.exomes.r2.1.1.sites.5.vcf.bgz.tbi
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diff --git a/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt b/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt
new file mode 100644
index 00000000..5eff2a13
--- /dev/null
+++ b/excerpt-data/03531c89f88e4ce8/genes_to_phenotype.txt
@@ -0,0 +1,3 @@
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+size 19753823
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new file mode 100644
index 00000000..1b1d952a
--- /dev/null
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+size 110
diff --git a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz b/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz
deleted file mode 100644
index 1a375af9..00000000
--- a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz
+++ /dev/null
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deleted file mode 100644
index 26926be6..00000000
--- a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi
+++ /dev/null
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deleted file mode 100644
index 41e6f387..00000000
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diff --git a/excerpt-data/05d48443127f19c1/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi b/excerpt-data/05d48443127f19c1/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi
deleted file mode 100644
index 2693dbcd..00000000
--- a/excerpt-data/05d48443127f19c1/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi
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deleted file mode 100644
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diff --git a/excerpt-data/05e93e6f1f5d60e6/gnomad.v4.0.sv.chr4.vcf.gz b/excerpt-data/05e93e6f1f5d60e6/gnomad.v4.0.sv.chr4.vcf.gz
deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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diff --git a/excerpt-data/0766243104b0c0b5/gnomad.genomes.v3.1.2.sites.chr7.vcf.bgz.tbi b/excerpt-data/0766243104b0c0b5/gnomad.genomes.v3.1.2.sites.chr7.vcf.bgz.tbi
index 07676d10..5ea3a18b 100644
--- a/excerpt-data/0766243104b0c0b5/gnomad.genomes.v3.1.2.sites.chr7.vcf.bgz.tbi
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version https://git-lfs.github.com/spec/v1
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diff --git a/excerpt-data/083f4075b9190a42/gnomad.exomes.v4.0.sites.chr10.vcf.bgz b/excerpt-data/083f4075b9190a42/gnomad.exomes.v4.0.sites.chr10.vcf.bgz
deleted file mode 100644
index 19b829b7..00000000
--- a/excerpt-data/083f4075b9190a42/gnomad.exomes.v4.0.sites.chr10.vcf.bgz
+++ /dev/null
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diff --git a/rules/output/annonars/alphamissense.smk b/rules/output/annonars/alphamissense.smk
index 9b3fc101..20abbde4 100644
--- a/rules/output/annonars/alphamissense.smk
+++ b/rules/output/annonars/alphamissense.smk
@@ -23,10 +23,10 @@ rule output_annonars_alphamissense: # -- build AlphaMissense RocksDB with annon
manifest=(
"output/full/annonars/alphamissense-{genome_release}-{v_alphamissense}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_alphamissense=RE_VERSION,
diff --git a/rules/output/annonars/cadd.smk b/rules/output/annonars/cadd.smk
index f10e9bce..9c649bb0 100644
--- a/rules/output/annonars/cadd.smk
+++ b/rules/output/annonars/cadd.smk
@@ -54,10 +54,10 @@ rule output_annonars_cadd: # -- build CADD RocksDB with annonars
),
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"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_cadd=RE_VERSION,
diff --git a/rules/output/annonars/cons.smk b/rules/output/annonars/cons.smk
index 788fe6fc..54e1bb15 100644
--- a/rules/output/annonars/cons.smk
+++ b/rules/output/annonars/cons.smk
@@ -12,10 +12,10 @@ rule output_annonars_cons: # -- build UCSC conservation track RocksDB with anno
),
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"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_cons=RE_VERSION,
diff --git a/rules/output/annonars/dbnsfp.smk b/rules/output/annonars/dbnsfp.smk
index 1873c76e..54386865 100644
--- a/rules/output/annonars/dbnsfp.smk
+++ b/rules/output/annonars/dbnsfp.smk
@@ -19,10 +19,10 @@ rule output_annonars_dbnsfp: # -- build dbNSFP RocksDB with annonars
manifest=(
"output/full/annonars/dbnsfp-{genome_release}-{v_dbnsfp}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_dbnsfp=RE_VERSION,
diff --git a/rules/output/annonars/dbscsnv.smk b/rules/output/annonars/dbscsnv.smk
index 9490149b..33350ee8 100644
--- a/rules/output/annonars/dbscsnv.smk
+++ b/rules/output/annonars/dbscsnv.smk
@@ -21,10 +21,10 @@ rule output_annonars_dbscsnv: # -- build dbscSNV RocksDB with annonars
manifest=(
"output/full/annonars/dbscsnv-{genome_release}-{v_dbscsnv}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_dbscsnv=RE_VERSION,
diff --git a/rules/output/annonars/dbsnp.smk b/rules/output/annonars/dbsnp.smk
index 52262544..bc1761d1 100644
--- a/rules/output/annonars/dbsnp.smk
+++ b/rules/output/annonars/dbsnp.smk
@@ -12,10 +12,10 @@ rule output_annonars_dbsnp: # -- build dbSNP RocksDB with annonars
),
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"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_dbsnp=RE_VERSION,
diff --git a/rules/output/annonars/gnomad_exomes.smk b/rules/output/annonars/gnomad_exomes.smk
index a4e12915..deb147ae 100644
--- a/rules/output/annonars/gnomad_exomes.smk
+++ b/rules/output/annonars/gnomad_exomes.smk
@@ -16,10 +16,10 @@ rule output_annonars_gnomad_exomes: # -- build gnomAD-exomes RocksDB with annon
manifest=(
"output/full/annonars/gnomad-exomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_gnomad=RE_VERSION,
diff --git a/rules/output/annonars/gnomad_genomes.smk b/rules/output/annonars/gnomad_genomes.smk
index 07c48251..1b885ca0 100644
--- a/rules/output/annonars/gnomad_genomes.smk
+++ b/rules/output/annonars/gnomad_genomes.smk
@@ -16,10 +16,10 @@ rule output_annonars_gnomad_genomes: # -- build gnomAD-genomes RocksDB with ann
manifest=(
"output/full/annonars/gnomad-genomes-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_gnomad=RE_VERSION,
diff --git a/rules/output/annonars/gnomad_mtdna.smk b/rules/output/annonars/gnomad_mtdna.smk
index befa299d..e9059ac8 100644
--- a/rules/output/annonars/gnomad_mtdna.smk
+++ b/rules/output/annonars/gnomad_mtdna.smk
@@ -16,10 +16,10 @@ rule output_annonars_gnomad_mtdna: # -- build gnomAD-mtDNA RocksDB with annonar
manifest=(
"output/full/annonars/gnomad-mtdna-{genome_release}-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_gnomad=RE_VERSION,
diff --git a/rules/output/annonars/gnomad_sv.smk b/rules/output/annonars/gnomad_sv.smk
index b5f1473d..33e2d246 100644
--- a/rules/output/annonars/gnomad_sv.smk
+++ b/rules/output/annonars/gnomad_sv.smk
@@ -15,10 +15,10 @@ rule output_annonars_gnomad_sv_grch37_exac: # -- build gnomAD-SV RocksDB with a
manifest=(
"output/full/annonars/gnomad-sv-exomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
v_gnomad=RE_VERSION,
v_annonars=RE_VERSION,
@@ -70,10 +70,10 @@ rule output_annonars_gnomad_sv_grch37_gnomad_sv2: # -- build gnomAD-SV RocksDB
manifest=(
"output/full/annonars/gnomad-sv-genomes-grch37-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
v_gnomad=RE_VERSION,
v_annonars=RE_VERSION,
@@ -123,10 +123,10 @@ rule output_annonars_gnomad_sv_grch38_gnomad_cnv4: # -- build gnomAD-SV RocksDB
manifest=(
"output/full/annonars/gnomad-sv-exomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
v_gnomad=RE_VERSION,
v_annonars=RE_VERSION,
@@ -175,10 +175,10 @@ rule output_annonars_gnomad_sv_grch38_gnomad_sv4: # -- build gnomAD-SV RocksDB
manifest=(
"output/full/annonars/gnomad-sv-genomes-grch38-{v_gnomad}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_gnomad=RE_VERSION,
diff --git a/rules/output/annonars/helix.smk b/rules/output/annonars/helix.smk
index b2db8c73..8ebcb24a 100644
--- a/rules/output/annonars/helix.smk
+++ b/rules/output/annonars/helix.smk
@@ -16,10 +16,10 @@ rule output_annonars_helixmtdb: # -- build HelixMtDb RocksDB with annonars
manifest=(
"output/full/annonars/helixmtdb-{genome_release}-{v_helixmtdb}+{v_annonars}/MANIFEST.txt",
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_helixmtdb=RE_VERSION,
diff --git a/rules/output/annonars/regions.smk b/rules/output/annonars/regions.smk
index fc178929..d6d4b114 100644
--- a/rules/output/annonars/regions.smk
+++ b/rules/output/annonars/regions.smk
@@ -13,7 +13,7 @@ rule work_annonars_regions_download: # -- download clingen regions
fi
wget -O {output} \
- ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_$GENOME.tsv
+ https://ftp.clinicalgenome.org/ClinGen_region_curation_list_$GENOME.tsv
"""
diff --git a/rules/output/mehari/freqs.smk b/rules/output/mehari/freqs.smk
index 2a5ebe28..7c112e3d 100644
--- a/rules/output/mehari/freqs.smk
+++ b/rules/output/mehari/freqs.smk
@@ -5,8 +5,8 @@ import os
rule output_mehari_freqs_build: # -- build frequency tables for mehari
input:
- gnomad_genomes="work/download/annos/{genome_release}/seqvars/gnomad_exomes/{v_gnomad_exomes}/.done",
- gnomad_exomes="work/download/annos/{genome_release}/seqvars/gnomad_genomes/{v_gnomad_genomes}/.done",
+ gnomad_genomes="work/download/annos/{genome_release}/seqvars/gnomad_genomes/{v_gnomad_genomes}/.done",
+ gnomad_exomes="work/download/annos/{genome_release}/seqvars/gnomad_exomes/{v_gnomad_exomes}/.done",
gnomad_mtdna="work/annos/{genome_release}/seqvars/gnomad_mtdna/{v_gnomad_mtdna}/gnomad_mtdna.vcf.gz",
helixmtdb="work/annos/{genome_release}/seqvars/helixmtdb/{v_helixmtdb}/helixmtdb.vcf.gz",
output:
@@ -22,10 +22,10 @@ rule output_mehari_freqs_build: # -- build frequency tables for mehari
"output/full/mehari/freqs-{genome_release}-{v_gnomad_genomes}+{v_gnomad_exomes}+"
"{v_gnomad_mtdna}+{v_helixmtdb}+{v_annonars}/MANIFEST.txt"
),
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
wildcard_constraints:
genome_release=RE_GENOME,
v_gnomad_genomes=RE_VERSION,
diff --git a/rules/output/viguno/hpo.smk b/rules/output/viguno/hpo.smk
index 5b0f87b8..8ebce33e 100644
--- a/rules/output/viguno/hpo.smk
+++ b/rules/output/viguno/hpo.smk
@@ -3,10 +3,6 @@
import os
-#: Number of threads to use for simulating in viguno.
-VIGUNO_SIMULATE_THREADS = int(os.environ.get("VIGUNO_SIMULATE_THREADS", 96))
-
-
rule output_viguno_pheno: # -- copy HPO
input:
obo="work/download/hpo/{v_hpo}/hp.obo",
@@ -19,9 +15,9 @@ rule output_viguno_pheno: # -- copy HPO
wildcard_constraints:
v_hpo=RE_VERSION,
v_viguno=RE_VERSION,
- threads: VIGUNO_SIMULATE_THREADS
+ threads: THREADS
resources:
- mem_mb_per_cpu="2GB",
+ mem_mb=MEMORY,
shell:
r"""
cp -a {input.obo} {output.obo}
diff --git a/rules/reduced/annonars.smk b/rules/reduced/annonars.smk
index 433de9a6..2069b18e 100644
--- a/rules/reduced/annonars.smk
+++ b/rules/reduced/annonars.smk
@@ -38,10 +38,10 @@ rule subset_annonars: # -- create exomes subset
genome_release=RE_GENOME,
v_hpo=RE_VERSION,
versions=RE_VERSION_MULTI,
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
shell:
r"""
annonars db-utils copy \
diff --git a/rules/reduced/hpo.smk b/rules/reduced/hpo.smk
index 374ef6d3..43c6825a 100644
--- a/rules/reduced/hpo.smk
+++ b/rules/reduced/hpo.smk
@@ -56,9 +56,9 @@ rule subset_worker_pheno_dev: # -- create development subset
wildcard_constraints:
v_hpo=RE_VERSION,
v_viguno=RE_VERSION,
- threads: VIGUNO_SIMULATE_THREADS
+ threads: THREADS
resources:
- mem_mb_per_cpu="2GB",
+ mem_mb=MEMORY,
shell:
r"""
cp -a {input.obo} {output.obo}
diff --git a/rules/reduced/mehari.smk b/rules/reduced/mehari.smk
index 5881f9d7..b523da08 100644
--- a/rules/reduced/mehari.smk
+++ b/rules/reduced/mehari.smk
@@ -37,10 +37,10 @@ rule subset_mehari: # -- create exomes subset
genome_release=RE_GENOME,
v_hpo=RE_VERSION,
versions=RE_VERSION_MULTI,
- threads: int(os.environ.get("THREADS_ANNONARS_IMPORT", "96"))
+ threads: THREADS
resources:
runtime=os.environ.get("RUNTIME_ANNONARS_IMPORT", "48h"),
- mem_mb_per_cpu=2000,
+ mem_mb=MEMORY,
shell:
r"""
annonars db-utils copy \
diff --git a/rules/work/annos/features/tads.smk b/rules/work/annos/features/tads.smk
index 19f38178..d4fe0aa6 100644
--- a/rules/work/annos/features/tads.smk
+++ b/rules/work/annos/features/tads.smk
@@ -14,7 +14,7 @@ rule annos_features_tads_download: # -- download TAD ZIP files from 3dgenome.or
wget --no-check-certificate \
-O {output.zip} \
- http://3dgenome.fsm.northwestern.edu/downloads/$name.TADs.zip
+ https://3dgenome.fsm.northwestern.edu/downloads/$name.TADs.zip
"""
diff --git a/rules/work/annos/seqvars/dbnsfp.smk b/rules/work/annos/seqvars/dbnsfp.smk
index 60038935..c27b2b57 100644
--- a/rules/work/annos/seqvars/dbnsfp.smk
+++ b/rules/work/annos/seqvars/dbnsfp.smk
@@ -54,7 +54,14 @@ rule annos_seqvars_dbnsfp_download: # -- download dbNSFP ZIP file
threads: 8
shell:
r"""
- url=https://dbnsfp.s3.amazonaws.com/dbNSFP4.5{wildcards.variant}.zip
+ url_a=https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l
+ url_c=https://usf.box.com/shared/static/03xsrpna0nzgrytfo2pzk326t8jad4oc
+
+ case "{wildcards.variant}" in
+ a) url=$url_a ;;
+ c) url=$url_c ;;
+ *) echo "Unsupported dbNSFP variant '{wildcards.variant}'" >&2; exit 1 ;;
+ esac
aria2c \
--check-certificate=false \
diff --git a/rules/work/annos/seqvars/dbscsnv.smk b/rules/work/annos/seqvars/dbscsnv.smk
index 4eeb31d4..92abb796 100644
--- a/rules/work/annos/seqvars/dbscsnv.smk
+++ b/rules/work/annos/seqvars/dbscsnv.smk
@@ -27,7 +27,7 @@ rule annos_seqvars_dbscsnv_download: # -- download dbscSNV ZIP file
--split=8 \
--max-concurrent-downloads=8 \
--max-connection-per-server=8 \
- ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbscSNV1.1.zip
+ https://usf.box.com/shared/static/ffwlywsat3q5ijypvunno3rg6steqfs8
"""
diff --git a/rules/work/annos/seqvars/gnomad_nuclear.smk b/rules/work/annos/seqvars/gnomad_nuclear.smk
index 716e0bb4..cab5a8c2 100644
--- a/rules/work/annos/seqvars/gnomad_nuclear.smk
+++ b/rules/work/annos/seqvars/gnomad_nuclear.smk
@@ -111,22 +111,24 @@ def input_annos_gnomad_nuclear_grch37(wildcards):
def input_annos_gnomad_nuclear_grch38(wildcards):
"""Input files for gnomAD exomes/genomes GRCh38."""
chroms = list(range(1, 23)) + ["X", "Y"]
- if wildcards.version == DV.gnomad_v4:
- tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz"
- return [tpl.format(chrom=chrom, **wildcards) for chrom in chroms]
- else:
- if wildcards.kind == "exomes":
- tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.r{version}.sites.{chrom}.liftover_grch38.vcf.bgz"
- return [
- tpl.format(kind=wildcards.kind, version=DV.gnomad_v2, chrom=chrom)
- for chrom in chroms
- ]
- else:
- tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz"
- return [
- tpl.format(kind=wildcards.kind, version=DV.gnomad_v3, chrom=chrom)
- for chrom in chroms
- ]
+ # if wildcards.version == DV.gnomad_v4:
+ tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz"
+ return [tpl.format(chrom=chrom, **wildcards) for chrom in chroms]
+
+
+# else:
+# if wildcards.kind == "exomes":
+# tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.r{version}.sites.{chrom}.liftover_grch38.vcf.bgz"
+# return [
+# tpl.format(kind=wildcards.kind, version=DV.gnomad_v2, chrom=chrom)
+# for chrom in chroms
+# ]
+# else:
+# tpl = "work/download/annos/grch38/seqvars/gnomad_{kind}/{version}/gnomad.{kind}.v{version}.sites.chr{chrom}.vcf.bgz"
+# return [
+# tpl.format(kind=wildcards.kind, version=DV.gnomad_v3, chrom=chrom)
+# for chrom in chroms
+# ]
rule annos_seqvars_gnomad_nuclear_grch37: # -- collect gnomAD exomes/genomes for GRCh37
diff --git a/rules/work/genes/clingen.smk b/rules/work/genes/clingen.smk
index d075f432..62883393 100644
--- a/rules/work/genes/clingen.smk
+++ b/rules/work/genes/clingen.smk
@@ -13,7 +13,7 @@ rule clingen_gene_download: # -- download files
fi
wget -O {output.tsv} \
- ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_{wildcards.genome_release}.tsv
+ https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_{wildcards.genome_release}.tsv
md5sum {output.tsv} > {output.tsv}.md5
"""
diff --git a/rules/work/genes/ensembl.smk b/rules/work/genes/ensembl.smk
index 8560c673..73a40a4b 100644
--- a/rules/work/genes/ensembl.smk
+++ b/rules/work/genes/ensembl.smk
@@ -9,19 +9,13 @@ rule genes_ensembl_create_xlink: # -- create ENSEMBL gene information xlink tab
r"""
# Check wehther ensembl version is correct.
export TMPDIR=$(mktemp -d)
- trap "rm -rf $TMPDIR" EXIT
- wget --no-check-certificate \
- -O $TMPDIR/current_README \
- https://ftp.ensembl.org/pub/current_README
- grep "The current release is Ensembl {DV.ensembl}" $TMPDIR/current_README \
- || (echo "Ensembl version is not {DV.ensembl}." && exit 1)
echo -e "ensembl_gene_id\tensembl_transcript_id\tentrez_id\tgene_symbol" \
>{output.tsv}
wget --no-check-certificate \
-O $TMPDIR/tmp \
- 'https://ensembl.org/biomart/martservice?query=' \
+ 'https://may2024.archive.ensembl.org/biomart/martservice?query=' \
sort -u $TMPDIR/tmp \
>> {output.tsv}
diff --git a/rules/work/genes/gnomad.smk b/rules/work/genes/gnomad.smk
index d13e2800..7261f505 100644
--- a/rules/work/genes/gnomad.smk
+++ b/rules/work/genes/gnomad.smk
@@ -161,6 +161,7 @@ def run_genes_gnomad_constraints_v4_to_tsv(input, output, wildcards):
> $TMPDIR/tmp.txt
# Select columns, rename, pad with the exac_* fields having NA values.
+ QSV_SKIP_FORMAT_CHECK=1 \
qsv select {columns_src_str} $TMPDIR/tmp.txt \
| qsv rename {columns_tmp_str} \
| perl -p -e 's/$/,exac_pLI,exac_obs_lof,exac_exp_lof,exac_oe_lof/ if $. == 1' \
diff --git a/rules/work/genes/hgnc.smk b/rules/work/genes/hgnc.smk
index 088f4fac..bb573d71 100644
--- a/rules/work/genes/hgnc.smk
+++ b/rules/work/genes/hgnc.smk
@@ -14,7 +14,7 @@ rule genes_hgnc_download: # -- Download the HGNC data
wget --no-check-certificate \
-O {output.json} \
- https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json
+ https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json
md5sum {output.json} > {output.json_md5}
"""
diff --git a/rules/work/genes/mehari_data_tx.smk b/rules/work/genes/mehari_data_tx.smk
index 8e2d4380..0bcf69f3 100644
--- a/rules/work/genes/mehari_data_tx.smk
+++ b/rules/work/genes/mehari_data_tx.smk
@@ -3,21 +3,21 @@
rule genes_mehari_data_tx_download: # -- Download the HGNC data
output:
- zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst",
+ zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst",
shell:
r"""
wget \
-O {output.zstd} \
- https://github.com/bihealth/mehari-data-tx/releases/download/v{wildcards.version}/mehari-data-txs-{wildcards.genome_release}-{wildcards.version}.bin.zst
+ https://github.com/bihealth/mehari-data-tx/releases/download/v{wildcards.version}/mehari-data-txs-{wildcards.genome_release}-{wildcards.refseq_or_ensembl}-{wildcards.version}.bin.zst
"""
rule genes_mehari_data_tx_copy: # -- Copy data to output
input:
- zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst",
+ zstd="work/download/mehari-data-tx/{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst",
output:
- zstd="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst",
- zstd_md5="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{version}.bin.zst.md5",
+ zstd="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst",
+ zstd_md5="output/full/mehari/genes-txs-{genome_release}-{version}/mehari-data-txs-{genome_release}-{refseq_or_ensembl}-{version}.bin.zst.md5",
shell:
r"""
cp {input.zstd} {output.zstd}
diff --git a/rules/work/genes/omim.smk b/rules/work/genes/omim.smk
index bb726eeb..c78b63a2 100644
--- a/rules/work/genes/omim.smk
+++ b/rules/work/genes/omim.smk
@@ -41,6 +41,7 @@ rule genes_omim: # -- prepare HGNC to OMIM disease mapping
echo hgnc_id,omim_id,disease_name \
> $TMPDIR/output.csv
+ QSV_SKIP_FORMAT_CHECK=1 \
qsv join -d '\t' \
omim_id $TMPDIR/mim2gene_hgnc.tsv \
database_id $TMPDIR/phenotype.hpoa \
diff --git a/rules/work/genes/rcnv.smk b/rules/work/genes/rcnv.smk
index 65556656..75fdcedf 100644
--- a/rules/work/genes/rcnv.smk
+++ b/rules/work/genes/rcnv.smk
@@ -24,6 +24,7 @@ rule genes_rcnv_postproces: # -- postprocess file for HGNC gene IDs
tsv_md5="work/genes/rcnv/2022/rcnv_collins_2022.tsv.md5",
shell:
"""
+ QSV_SKIP_FORMAT_CHECK=1 \
qsv join -d '\t' \
'#gene' <(zcat {input.tsv}) \
gene_symbol {input.xlink} \
diff --git a/rules/work/genes/shet.smk b/rules/work/genes/shet.smk
index b0204a39..d28eca14 100644
--- a/rules/work/genes/shet.smk
+++ b/rules/work/genes/shet.smk
@@ -9,6 +9,7 @@ rule genes_shet: # -- postprocess file for HGNC gene IDs
tsv="work/genes/shet/2019/shet_weghorn_2019.tsv",
shell:
"""
+ QSV_SKIP_FORMAT_CHECK=1 \
qsv join -d '\t' \
'Gene' <(zcat {input.tsv}) \
gene_symbol {input.xlink} \
diff --git a/scripts/genes-integrate-diseases.py b/scripts/genes-integrate-diseases.py
index da42e183..3fcdb277 100644
--- a/scripts/genes-integrate-diseases.py
+++ b/scripts/genes-integrate-diseases.py
@@ -145,6 +145,8 @@ class Aspect(enum.Enum):
CLINICAL_COURSE = "C"
#: Modifier
CLINICAL_MODIFIER = "M"
+ #: Past medical history
+ PAST_MEDICAL_HISTORY = "H"
class HpoaEntry(BaseModel):
diff --git a/scripts/genes-orpha-diseases.py b/scripts/genes-orpha-diseases.py
index ad9a426c..9dc7c03d 100755
--- a/scripts/genes-orpha-diseases.py
+++ b/scripts/genes-orpha-diseases.py
@@ -36,7 +36,9 @@ async def work(no: int, orpha_id: int, limiter: trio.CapacityLimiter):
async with limiter:
async with httpx.AsyncClient() as client:
try:
- cross_references = (await client.get(URL_ORPHACODE_GET.format(orpha_id))).json()
+ cross_references = (
+ await client.get(URL_ORPHACODE_GET.format(orpha_id), timeout=60)
+ ).json()
disease_genes = (
await client.get(URL_ORPHACODE_GET_GENE.format(orpha_id), timeout=60)
).json()
diff --git a/utils/install-annonars.sh b/utils/install-annonars.sh
deleted file mode 100644
index 03515482..00000000
--- a/utils/install-annonars.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-image="ghcr.io/varfish-org/annonars:0.41.3"
-source_path="/usr/local/bin/annonars"
-destination_path="/usr/local/bin/annonars"
-
-container_id=$(docker create "$image")
-docker cp "$container_id:$source_path" "$destination_path"
-docker rm "$container_id"
diff --git a/varfish_db_downloader/versions.py b/varfish_db_downloader/versions.py
index 389580b7..b4df3eb2 100644
--- a/varfish_db_downloader/versions.py
+++ b/varfish_db_downloader/versions.py
@@ -11,7 +11,7 @@
#: Allow to disable the today check.
FORCE_TODAY = os.environ.get("FORCE_TODAY", "false").lower() == "true"
#: The ClinVar release to use (includes annonars version used for building).
-CLINVAR_RELEASE = os.environ.get("CLINVAR_RELEASE", "20240612+0.17.0")
+CLINVAR_RELEASE = os.environ.get("CLINVAR_RELEASE", "20250410+0.18.5")
#: The ClinVar version to use (part of the tag and release name).
CLINVAR_VERSION = CLINVAR_RELEASE.replace("-", "").split("+")[0]
@@ -127,10 +127,10 @@ class DataVersions:
clingen_gene=TODAY,
clingen_variant=TODAY,
ensembl_37="87",
- ensembl_38="112",
- ensembl="112",
+ ensembl_38="112", # keep at 112 for consistency with mehari
+ ensembl="112", # keep at 112 for consistency with mehari
today=TODAY,
- dbnsfp="4.5",
+ dbnsfp="4.5", # update to 4.9 or 5.1 ?
dbscsnv="1.1",
cadd="1.6",
gnomad_constraints="4.1",
@@ -161,10 +161,10 @@ class DataVersions:
refseq_38="GCF_000001405.40+RS_2023_03",
dbsnp="b151",
acmg_sf="3.1",
- hpo="20240116",
+ hpo="20250303",
orphadata=TODAY,
patho_mms="20220730",
- mehari_tx="0.4.4",
+ mehari_tx="0.10.3",
clinvar_release=CLINVAR_RELEASE,
clinvar_version=CLINVAR_VERSION,
tracks="0",
diff --git a/varfish_db_downloader/wget.py b/varfish_db_downloader/wget.py
index 36cb6591..49bbef4c 100644
--- a/varfish_db_downloader/wget.py
+++ b/varfish_db_downloader/wget.py
@@ -1,5 +1,6 @@
"""Implementation of the stub ``wget`` and supporting tool."""
+import cgi
import gzip
import hashlib
import itertools
@@ -21,6 +22,63 @@
from loguru import logger
+def get_proxies_from_env() -> dict[str, str]:
+ proxies = {}
+ ftp_proxy = os.environ.get("ftp_proxy") or os.environ.get("FTP_PROXY")
+ no_proxy = os.environ.get("no_proxy") or os.environ.get("NO_PROXY")
+ if ftp_proxy:
+ proxies["ftp"] = ftp_proxy
+ if no_proxy:
+ # If no_proxy is set, we need to ensure it is in the right format
+ # for requests, which expects a comma-separated list.
+ proxies["no_proxy"] = no_proxy.replace(",", ";")
+ return proxies or {}
+
+
+def get_filename_from_url(url: str) -> str | None:
+ """
+ Extracts the filename from a URL.
+
+ First, it tries to get the filename from the 'Content-Disposition' header.
+ If not found, it falls back to parsing the URL path.
+
+ Args:
+ url: The URL of the file to inspect.
+
+ Returns:
+ The detected filename as a string, or None if an error occurs
+ or no filename can be found.
+ """
+ try:
+ # We use stream=True to avoid downloading the file content
+ with requests.get(url, allow_redirects=True, stream=True) as response:
+ # Raise an exception for bad status codes (4xx or 5xx)
+ response.raise_for_status()
+
+ # 1. Check for Content-Disposition header
+ content_disposition = response.headers.get("content-disposition")
+ if content_disposition:
+ # Parse the header to extract the filename
+ _, params = cgi.parse_header(content_disposition)
+ if "filename" in params:
+ return params["filename"]
+
+ # 2. If no header, fall back to the URL path
+ path = urllib.parse.urlparse(
+ response.url
+ ).path # Use response.url to get the final URL after redirects
+ filename = os.path.basename(path)
+ if filename:
+ return filename
+
+ except requests.exceptions.RequestException as e:
+ print(f"Error fetching URL: {e}")
+ return None
+
+ # 3. If all else fails
+ return None
+
+
def excerpt_manual(url: str, path_out: str, count: int):
"""Do not download, assume output is already there."""
_ = url
@@ -34,10 +92,11 @@ def no_excerpt(url: str, path_out: str, count: int):
"""Do not excerpt, use all."""
logger.info(" (strategy no-excerpt from {} to {})", url, path_out)
_ = count
+ proxies = get_proxies_from_env()
with open(path_out, "wb") as outputf:
requests_ftp.monkeypatch_session()
s = requests.Session()
- r = s.get(url, allow_redirects=True)
+ r = s.get(url, proxies=proxies, allow_redirects=True)
outputf.write(r.content)
@@ -52,15 +111,18 @@ def decompress_stream(stream):
def excerpt_head(url: str, path_out: str, count: int):
"""Excerpt a plaint-text file by copying lines."""
logger.info(" (strategy head from {} to {})", url, path_out)
- try_gzip = url.endswith(".gz") or url.endswith(".bgz")
+ is_gz = url.endswith(".gz")
+ is_bgz = url.endswith(".bgz")
+ try_gzip = is_gz or is_bgz
if try_gzip:
opener = gzip.open
else:
opener = open
+ proxies = get_proxies_from_env()
with opener(path_out, "wb") as f_out:
requests_ftp.monkeypatch_session()
s = requests.Session()
- r = s.get(url, stream=True)
+ r = s.get(url, proxies=proxies, stream=True)
# First, attempt to read line by line which should work if requests is
# correctly identifying gzip compression.
is_raw_gzip = False
@@ -87,7 +149,7 @@ def excerpt_head(url: str, path_out: str, count: int):
break
f_out.write(line.encode("utf-8"))
f_out.write(b"\n")
- if try_gzip:
+ if is_gz:
# Fixup resulting compressed files so they are proper bgzip.
subprocess.check_call(["gzip", "-d", path_out])
subprocess.check_call(["bgzip", path_out.replace(".gz", "")])
@@ -95,16 +157,18 @@ def excerpt_head(url: str, path_out: str, count: int):
def excerpt_copy_tbi(url: str, path_out: str, count: int):
"""Copy ``.tbi`` file from the (previously downloaded) ``.vcf.gz`` file.)"""
+ logger.info(" (performing download before COPY-TSV from {} to {})", url, path_out)
+ no_excerpt(url, path_out, count)
_ = count
vcf_url = url[:-4]
vcf_file = vcf_url.split("/")[-1]
vcf_url_hash = hash_url(vcf_url)
base_path = os.path.dirname(os.path.dirname(path_out))
vcf_tbi_path = f"{base_path}/{vcf_url_hash}/{vcf_file}.tbi"
- logger.info(" (strategy COPY_TBI from {} to {})", vcf_tbi_path, path_out)
- if not os.path.exists(vcf_tbi_path):
- raise RuntimeError(f"File {vcf_tbi_path} does not exist (strategy COPY-TBI)")
- shutil.copy(vcf_tbi_path, path_out)
+ if not os.path.exists(path_out):
+ raise RuntimeError(f"File {path_out} does not exist (strategy COPY-TBI)")
+ logger.info(" (strategy COPY_TBI from {} to {})", path_out, vcf_tbi_path)
+ shutil.copy(path_out, vcf_tbi_path)
def excerpt_vcf_head(url: str, path_out: str, count: int):
@@ -233,8 +297,7 @@ def download_excerpt(url: UrlEntry, data_dir: str, force: bool):
print(url.url, file=f)
excerpt_fun = STRATEGY_MAP[url.excerpt_strategy.strategy]
- parsed = urllib.parse.urlparse(url.url)
- basename = parsed.path.split("/")[-1] or "__index__"
+ basename = get_filename_from_url(url.url) or "__index__"
out_path_data = str(out_path / basename)
logger.info(" getting excerpt to {}", out_path_data)
excerpt_fun(url.url, str(out_path_data), url.excerpt_strategy.count)
@@ -246,8 +309,7 @@ def copy_excerpt(url: UrlEntry, data_dir: str, output_document: str):
"""Copy downloaded excerpt to output file."""
logger.info(" copying excerpt for {} to {}", url.url, output_document)
in_path = pathlib.Path(data_dir) / url.hash
- parsed = urllib.parse.urlparse(url.url)
- basename = parsed.path.split("/")[-1]
+ basename = get_filename_from_url(url.url) or "__index__"
excerpt_path = in_path / basename
click.echo(err=True, message="copying {} => {}".format(excerpt_path, output_document))
if os.path.isdir(excerpt_path):