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

varfish-org · Jul 18, 2024 · 6a29e38 · 6a29e38
1 parent 871af29
commit 6a29e38
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Showing 3 changed files with 56 additions and 6 deletions.
diff --git a/Snakefile b/Snakefile
@@ -276,24 +276,42 @@ rule all:
         f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
         # -- annonars
         f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
+        f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
+        f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml",
+        f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
         # -- mehari
         f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
         f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
         #
         # == exomes (reduced data) directories ==================================================
         #
@@ -307,24 +325,42 @@ rule all:
         f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
         # -- annonars
         f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbnsfp-grch37-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
+        f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}a+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/spec.yaml",
+        f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbsnp-grch37-{DV.dbsnp}+{PV.annonars}/spec.yaml",
+        f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/dbsnp-grch38-{DV.dbsnp}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/spec.yaml",
         # -- mehari
         f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
         f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/spec.yaml",
 
 
 # ===============================================================================================

diff --git a/rules/reduced/annonars.smk b/rules/reduced/annonars.smk
@@ -18,6 +18,10 @@ def input_subset_annonars(wildcards):
             f"output/full/annonars/{wildcards.name}-{wildcards.genome_release}-"
             f"{wildcards.version_multi}/rocksdb/IDENTITY"
         ),
+        "spec_yaml": (
+            f"output/full/annonars/{wildcards.name}-{wildcards.genome_release}-"
+            f"{wildcards.version_multi}/spec.yaml"
+        ),
     }
     return result
 
@@ -27,6 +31,7 @@ rule subset_annonars:  # -- create exomes subset
         unpack(input_subset_annonars),
     output:
         rocksdb_identity="output/reduced-{set_name}/annonars/{name}-{genome_release}-{version_multi}/rocksdb/IDENTITY",
+        spec_yaml="output/reduced-{set_name}/annonars/{name}-{genome_release}-{version_multi}/spec.yaml",
     wildcard_constraints:
         name=RE_NAME,
         genome_release=RE_GENOME,
@@ -44,4 +49,6 @@ rule subset_annonars:  # -- create exomes subset
             --path-in $(dirname {input.rocksdb_identity}) \
             --path-out $(dirname {output.rocksdb_identity}) \
             --path-beds {input.bed}
+
+        cp {input.spec_yaml} {output.spec_yaml}
         """
diff --git a/rules/reduced/mehari.smk b/rules/reduced/mehari.smk
@@ -18,6 +18,10 @@ def input_subset_mehari(wildcards):
             f"output/full/mehari/freqs-{wildcards.genome_release}-"
             f"{wildcards.version_multi}/rocksdb/IDENTITY"
         ),
+        "spec_yaml": (
+            f"output/full/mehari/freqs-{wildcards.genome_release}-"
+            f"{wildcards.version_multi}/spec.yaml"
+        ),
     }
     return result
 
@@ -27,6 +31,7 @@ rule subset_mehari:  # -- create exomes subset
         unpack(input_subset_mehari),
     output:
         rocksdb_identity="output/reduced-{set_name}/mehari/freqs-{genome_release}-{version_multi}/rocksdb/IDENTITY",
+        spec_yaml="output/reduced-{set_name}/mehari/freqs-{genome_release}-{version_multi}/spec.yaml",
     wildcard_constraints:
         genome_release=RE_GENOME,
         v_hpo=RE_VERSION,
@@ -41,4 +46,6 @@ rule subset_mehari:  # -- create exomes subset
             --path-in $(dirname {input.rocksdb_identity}) \
             --path-out $(dirname {output.rocksdb_identity}) \
             --path-beds {input.bed}
+
+        cp {input.spec_yaml} {output.spec_yaml}
         """