From 71634f1f726c45d6688956ec50010b2d64ee09f8 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:15:32 +0000
Subject: [PATCH 1/3] Update to PopPUNK GPS v9 database
---
nextflow.config | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
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
From 7eeacace9dc663981204784f277b480f0a8a2c6c Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:42:22 +0000
Subject: [PATCH 2/3] Update default PopPUNK database information
---
README.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 40a16c4..19f30c5 100644
--- a/README.md
+++ b/README.md
@@ -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 |
From 8de9013a805aabfba263f69e5b74674730bfa304 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:43:58 +0000
Subject: [PATCH 3/3] Update storage requirement
---
README.md | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/README.md b/README.md
index 19f30c5..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))