diff --git a/README.md b/README.md index 40a16c4..a28b316 100644 --- a/README.md +++ b/README.md @@ -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
(These files can be removed when the pipeline run is completed, please refer to [Clean Up](#clean-up))
(To further reduce storage requirement by sacrificing the ability to resume the pipeline, please refer to [Experimental](#experimental)) @@ -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
(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
(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
(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
(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 | diff --git a/nextflow.config b/nextflow.config index 7ae5594..983433a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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