From 8a781b6bb2267cca0b1d4ec87da2a7c577e69906 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 12:54:07 +0200 Subject: [PATCH] modify alternative module load --- docs/ku_sund_dangpu.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 92e73b5..f63aa0c 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -13,7 +13,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -# alternative module load jdk/1.8.0_291 nextflow/22.04.3 singularity/3.8.0 +# alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0 export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/tmp @@ -26,7 +26,9 @@ mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` +Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the ku_sund_dangpu profile. Just make sure that the pipeline is run within a tmux session. + ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` +