From b16b011bcc2fc72ad7b3b84b410d895cae139cdf Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Thu, 22 Apr 2021 12:02:11 +0100 Subject: [PATCH] Add ~/bin as recommended location for nextflow executable --- docs/sanger.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/sanger.md b/docs/sanger.md index bb0e607..483683c 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -11,6 +11,8 @@ The latest version of Nextflow is not installed by default on the cluster. You w - Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) +Recommendation place to move the `nextflow` executable is `~/bin` so that it's in the `PATH`. + Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command. Nextflow shouldn't run directly on the submission node but on a compute node. To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh` @@ -27,10 +29,10 @@ export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128' export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128' export NXF_ANSI_LOG=false export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000" -export NXF_VER=21.03.0-edge +export NXF_VER=21.04.0-edge -/path/to/your/install/nextflow run \ +nextflow run \ /path/to/nf-core/pipeline/main.nf \ -w /path/to/some/dir/work \ -profile sanger \