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

Jump to bottom

Update PopPUNK Database to GPS v9 #114

Merged
merged 5 commits into from
Jul 30, 2024
Merged

Update PopPUNK Database to GPS v9 #114

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
957d96b
Merge pull request #111 from sanger-bentley-group/dev
HarryHung Jun 13, 2024
951e417
Merge pull request #112 from sanger-bentley-group/dev
HarryHung Jun 13, 2024
71634f1
Update to PopPUNK GPS v9 database
HarryHung Jul 29, 2024
7eeacac
Update default PopPUNK database information
HarryHung Jul 29, 2024
8de9013
Update storage requirement
HarryHung Jul 29, 2024
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
8 changes: 4 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69,10 +69,10 @@ The development of this pipeline is part of the GPS Project ([Global Pneumococca
- [Docker Desktop on Windows with WSL](https://docs.docker.com/desktop/wsl/) by Docker

### Hardware
It is recommended to have at least 16GB of RAM and 50GB of free storage
It is recommended to have at least 16GB of RAM and 100GB of free storage
> ℹ️ Details on storage
> - The pipeline core files use ~5MB
> - All default databases use ~8GB in total
> - All default databases use ~19GB in total
> - All Docker images use ~13GB in total; alternatively, Singularity images use ~4.5GB in total
> - The pipeline generates ~1.8GB intermediate files for each sample on average<br>(These files can be removed when the pipeline run is completed, please refer to [Clean Up](#clean-up))<br>
(To further reduce storage requirement by sacrificing the ability to resume the pipeline, please refer to [Experimental](#experimental))
Expand Down Expand Up @@ -255,8 +255,8 @@ The pipeline is compatible with [Launchpad](https://docs.seqera.io/platform/late
## Lineage
| Option | Values | Description |
| --- | ---| --- |
| `--poppunk_db_remote` | Any valid URL to a PopPUNK database in `.tar.gz` or `.tgz` format<br />(Default: [GPS v8 - Reference Only](https://gps-project.cog.sanger.ac.uk/GPS_v8_ref.tar.gz)) | URL to a PopPUNK database. |
| `--poppunk_ext_remote` | Any valid URL to a PopPUNK external clusters file in `.csv` format<br />(Default: [GPS v8 GPSC Designation](https://gps-project.cog.sanger.ac.uk/GPS_v8_external_clusters.csv)) | URL to a PopPUNK external clusters file. |
| `--poppunk_db_remote` | Any valid URL to a PopPUNK database in `.tar.gz` or `.tgz` format<br />(Default: [GPS v9](https://gps-project.cog.sanger.ac.uk/GPS_v9.tar.gz)) | URL to a PopPUNK database. |
| `--poppunk_ext_remote` | Any valid URL to a PopPUNK external clusters file in `.csv` format<br />(Default: [GPS v9 GPSC Designation](https://gps-project.cog.sanger.ac.uk/GPS_v9_external_clusters.csv)) | URL to a PopPUNK external clusters file. |

## Other AMR
| Option | Values | Description |
Expand Down
4 changes: 2 additions & 2 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@ params {
ref_genome = "$projectDir/data/ATCC_700669_v1.fa"

// Default links for PopPUNK Database and External Clusters
poppunk_db_remote = "https://gps-project.cog.sanger.ac.uk/GPS_v8_ref.tar.gz"
poppunk_ext_remote = "https://gps-project.cog.sanger.ac.uk/GPS_v8_external_clusters.csv"
poppunk_db_remote = "https://gps-project.cog.sanger.ac.uk/GPS_v9.tar.gz"
poppunk_ext_remote = "https://gps-project.cog.sanger.ac.uk/GPS_v9_external_clusters.csv"

// Default values for QC
spneumo_percentage = 60.00
Expand Down