From d9a800966213d301dd4f2c402169d4db0faf40e7 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 25 Nov 2020 22:45:16 +0100 Subject: [PATCH 1/2] Better UPPMAX docs --- docs/uppmax.md | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 0f23cd1..8551067 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -2,6 +2,10 @@ All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters. +## Getting help + +We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https://nfcore.slack.com/channels/uppmax](https://nfcore.slack.com/channels/uppmax) + ## Using the UPPMAX config profile To use, run the pipeline with `-profile uppmax` (one hyphen). @@ -12,14 +16,19 @@ In addition to this config profile, you will also need to specify an UPPMAX proj You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: ```bash -nextflow run nf-core/PIPELINE -profile uppmax --project SNIC 2018/1-234 # ..rest of pipeline flags +nextflow run nf-core/PIPELINE -profile uppmax --project "snic2018-1-234" # ..rest of pipeline flags ``` +> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR. + Before running the pipeline you will need to either install Nextflow or load it using the environment module system. -This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler. +This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler and using Singularity for software management. + Just run Nextflow on a login node and it will handle everything else. +Remember to use `-bg` to launch Nextflow in the background, so that the pipeline doesn't exit if you leave your terminal session. + ## Using iGenomes references A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`. @@ -40,7 +49,7 @@ Note that each job will still start with the same request as normal, but restart All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances. -## How to specify a UPPMAX cluster +## Different UPPMAX clusters The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits: From e96455e1809cdb0221fbbec502b933b8664978c1 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 26 Nov 2020 01:43:09 +0100 Subject: [PATCH 2/2] Update docs/uppmax.md --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index 8551067..dcd6ca0 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -16,7 +16,7 @@ In addition to this config profile, you will also need to specify an UPPMAX proj You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: ```bash -nextflow run nf-core/PIPELINE -profile uppmax --project "snic2018-1-234" # ..rest of pipeline flags +nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags ``` > NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.