# Running [nf-core](https://nf-co.re/) pipelines/ [Nextflow](https://www.nextflow.io/) on Rackham and Bianca :::danger The nf-core pipelines are not supported anymore at UPPMAX. To learn how to download your pipeline for offline use on Bianca, please follow this tutorial [nf-core pipelines on Bianca](https://hackmd.io/@pmitev/nfcore_pipelines_Bianca) instead. ::: [TOC] ## 1. Available modules i. Load the **bioinfo-tools** module tree ```bash $ module load bioinfo-tools ``` ii. Related modules and versions as of 2023.04.24 ```bash $ module avail Nextflow -------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines --------------------------------------------------- Nextflow/latest Nextflow/0.26.0 Nextflow/19.01.0 Nextflow/20.10.0 Nextflow/21.04.1 Nextflow/22.10.1 (D) Nextflow/0.17.3 Nextflow/0.31.1 Nextflow/20.02.0-edge Nextflow/21.01.0-edge Nextflow/21.10.6 Nextflow/0.22.2 Nextflow/18.10.1 Nextflow/20.04.0-edge Nextflow/21.02.0-edge Nextflow/22.10.0 $ module avail nf-core/ -------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines --------------------------------------------------- nf-core/latest nf-core/1.12.1 nf-core/1.14 nf-core/2.1 nf-core/2.4.1 nf-core/2.6 (D) $ module avail nf-core-pipelines -------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines --------------------------------------------------- nf-core-pipelines/latest ``` Load the **nf-core-pipelines** module. The module will load the correct versions for `Nextflow`, `java`, and `nf-core` automatically. ```bash $ module load bioinfo-tools nf-core-pipelines $ module list Currently Loaded Modules: 1) uppmax 2) bioinfo-tools 3) java/OracleJDK_11.0.9 4) Nextflow/22.10.0 5) nf-core-pipelines/latest ``` If you want, after this you can load the latest *Nextflow* version with `module load Nextflow/latest` ## 2. Test: Running sarek v3.1.2 For convenience, all stable versions of the official *nf-core* pipelines are mirrored locally and most of the required Singularity containers are also available. Start an interactive job. ```bash $ interactive -A nais2023-1-123 -p core -n 1 -t 10-00:00:00 ``` Interactive jobs on Rackham and Bianca are running withing `screen` session, which ensures that the program will continue running even if you lose connection to the cluster or the session is closed because of inactivity in the shell. ```bash $ nextflow run $NF_CORE_PIPELINES/sarek/3.1.2/workflow --project nais2023-1-123 -profile uppmax,test --outdir outdir ... -[nf-core/sarek] Pipeline completed successfully- Completed at: 24-Apr-2023 16:11:53 Duration : 1h 38m 25s CPU hours : 0.1 Succeeded : 26 ``` :notebook: Have a look at https://github.com/nf-core/configs/blob/master/docs/uppmax.md for detailed instructions on running *nf-core* on UPPMAX and hints on additional options. Note the small difference when loading the modules. :gear: https://github.com/nf-core/configs/blob/master/conf/uppmax.config details on the predefined uppmax profile. ## 3. Troubleshooting Check that you have somewhat reasonable environment before running nextflow. ```bash $ env | grep 'NXF_\|NF_' NXF_HOME=/home/USER/.nextflow NXF_TEMP=/scratch/USER NXF_SINGULARITY_LIBRARYDIR=/sw/bioinfo/nf-core-pipelines/latest/rackham/singularity_cache_dir NXF_LAUNCHER=/scratch NXF_DIST=/sw/bioinfo/Nextflow/22.10.0/rackham/nxf_home/framework NF_CORE_PIPELINES=/sw/bioinfo/nf-core-pipelines/latest/rackham NF_CORE_PIPELINES_ROOT=/sw/bioinfo/nf-core-pipelines/latest/rackham ``` Check that you have space to run the calculations. ```bash $ uquota Your project Your File Area Unit Usage Quota Limit Over Quota --------------- ------------------- -------- ------- ----------- ---------- home /home/USER GBytes 10.2 32.0 home /home/USER Files 165979 300000 naiss2023-22-21 /proj/introtouppmax GBytes 3.7 128 snic2022-5-301 /proj/snic_ae GBytes 0.0 128 ``` ## Contacts: - [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425) - [UPPMAX](https://www.uppmax.uu.se/) - [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ) ###### tags: `UPPMAX`,`nextflow`,`nf-core`