adjustments

Author: holtgrewe

Snakefile

@@ -207,6 +207,8 @@ rule all:
         # -- annonars
         f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
+        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/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
@@ -215,8 +217,6 @@ rule all:
         f"output/reduced-dev/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
@@ -236,6 +236,8 @@ rule all:
         # -- annonars
         f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
+        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/dbnsfp-grch37-{DV.dbnsfp}a+{PV.annonars}/rocksdb/IDENTITY",
@@ -244,8 +246,6 @@ rule all:
         f"output/reduced-exomes/annonars/dbnsfp-grch38-{DV.dbnsfp}c+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",

environment.yml

@@ -44,3 +44,5 @@ dependencies:
   - viguno =0.1.6
   - mehari =0.5.7
   - varfish-server-worker =0.7.0
+  # S3 uploads
+  - s5cmd =2.1.0