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fix: bump cdot to 0.2.27, snakemake wrappers #58

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Nov 26, 2024
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fix: bump cdot to 0.2.27, snakemake wrappers #58

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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -8,10 +8,10 @@ This repository contains a snakemake workflow to build mehari transcript databas

Databases are built for each combination of genome release (GRCh37, GRCh38) and reference source (ensembl, refseq):

- mehari-data `v0.7.0`
- mehari-data `v0.9.0`
- uses:
- mehari `v0.26.1`
- cdot: `v0.2.26`
- mehari `v0.30.1`
- cdot: `v0.2.27`
- `GRCh37-refseq`
- genome release: GRCh37.p13
- VEP/ENSEMBL equivalent: `105`
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12 changes: 6 additions & 6 deletions config/config.yaml
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Expand Up @@ -27,7 +27,7 @@ reference:
sources:
GRCh38-refseq:
cdot:
release: 0.2.26
release: 0.2.27
custom: GCF_000001405.40_GRCh38.p14_genomic.110.gff
known_issues:
- id_type: gene_symbol
Expand Down Expand Up @@ -110,7 +110,7 @@ sources:

GRCh37-refseq:
cdot:
release: 0.2.26
release: 0.2.27
custom: GCF_000001405.25_GRCh37.p13_genomic.105.20201022.gff
known_issues:
- id_type: gene_symbol
Expand Down Expand Up @@ -151,8 +151,8 @@ sources:
# (rules::cdot::cdot_chrMT expects 'GRCh38-ensembl' to be defined)
GRCh38-ensembl:
cdot:
release: 0.2.26
custom: ensembl.Homo_sapiens.GRCh38.112.gff3
release: 0.2.27
custom: ensembl.Homo_sapiens.GRCh38.112.gtf
known_issues:
- id_type: hgnc_id
id: "HGNC:32925"
Expand Down Expand Up @@ -213,8 +213,8 @@ sources:
description: novel gene/transcript without HGNC id
GRCh37-ensembl:
cdot:
release: 0.2.26
custom: ensembl.Homo_sapiens.GRCh37.87.gff3
release: 0.2.27
custom: ensembl.Homo_sapiens.GRCh37.87.gtf
known_issues:
- id_type: gene_symbol
id: "ATXN8"
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2 changes: 1 addition & 1 deletion workflow/rules/download.smk
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Expand Up @@ -10,7 +10,7 @@ rule get_ensembl_sequence:
"logs/{assembly}-ensembl/get_ensembl_sequence.{datatype}.log",
cache: "omit-software" # save space and time with between workflow caching (see docs)
wrapper:
"v3.11.0/bio/reference/ensembl-sequence"
"v5.0.2/bio/reference/ensembl-sequence"


rule merge_ensembl_sequence:
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2 changes: 1 addition & 1 deletion workflow/rules/validate.smk
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Expand Up @@ -79,4 +79,4 @@ rule datavzrd:
log:
"logs/datavzrd_report/{assembly}-{source}/seqrepo/check_mehari_db.log",
wrapper:
"v3.13.1/utils/datavzrd"
"v5.0.2/utils/datavzrd"
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