Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FIX: remove check annotation folders existence when no annotation #1236

Merged
merged 8 commits into from
Sep 15, 2023
Merged

FIX: remove check annotation folders existence when no annotation #1236

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
b2dde77
update CHANGELOG
maxulysse Sep 15, 2023
15206c9
fixing folder checks
maxulysse Sep 15, 2023
841ed94
add meta map to channel
maxulysse Sep 15, 2023
09553a7
more complete error message
maxulysse Sep 15, 2023
9e27d77
fix map
maxulysse Sep 15, 2023
0918d31
simplify logic
maxulysse Sep 15, 2023
ed0e052
more safeguards
maxulysse Sep 15, 2023
e745db6
code polish
maxulysse Sep 15, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed

- [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
- [#1236](https://github.com/nf-core/sarek/pull/1236) - Fix annotation cache folder verification when no annotation

### Dependencies

Expand Down
15 changes: 8 additions & 7 deletions workflows/sarek.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -288,19 +288,20 @@ if ((params.download_cache) && (params.snpeff_cache || params.vep_cache)) {
error("Please specify either `--download_cache` or `--snpeff_cache`, `--vep_cache`.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
}

if ( params.vep_cache ) {
if (params.snpeff_cache && params.tools && params.tools.contains("snpeff")) {
def snpeff_cache_dir = file("$params.snpeff_cache", type: 'dir') / "${params.snpeff_genome}.${params.snpeff_db}"
if ( !snpeff_cache_dir.exists() || !snpeff_cache_dir.isDirectory() ) {
error("Files within --snpeff_cache invalid. Make sure there is a directory named ${params.snpeff_genome}.${params.snpeff_db} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
}
}

if (params.vep_cache && params.tools && params.tools.contains("vep")) {
def vep_cache_dir = file("$params.vep_cache", type: 'dir') / "${params.vep_cache_version}_${params.vep_genome}"
if ( !vep_cache_dir.exists() || !vep_cache_dir.isDirectory() ) {
error("Files within --vep_cache invalid. Make sure there is a directory named ${params.vep_cache_version}_${params.vep_genome} in ${params.vep_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
}
}

if ( params.snpeff_cache ) {
def snpeff_cache_dir = file("$params.snpeff_cache", type: 'dir') / "${params.snpeff_genome}.${params.snpeff_db}"
if ( !snpeff_cache_dir.exists() || !snpeff_cache_dir.isDirectory() ) {
error("Files within --snpeff_cache invalid. Make sure there is a directory named ${params.snpeff_genome}.${params.snpeff_db} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation")
}
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
Expand Down