# BACTpipe on Dardel
> or any other cluster running `SLURM` and `Singularity`/`Apptainer`

## General setup

# Load relevant modules
$ module load PDC/23.12 java/17.0.4 singularity anaconda3

# make bin folder and add "export PATH+=$HOME/bin" in ~/.bashrc
$ mkdir -p $HOME/bin
$ cd $HOME/bin
$ export PATH+=:$HOME/bin

## :computer: nextflow

# Install Nextflow
$ cd ~/bin
$ curl -s https://get.nextflow.io | bash

## pipeline config
Create file `containers.config` with the following content.

// vim: syntax=groovy expandtab
// BACTpipe Nextflow configuration file

process {
    errorStrategy = 'ignore'
    executor = 'slurm'
    //executor = 'local'
    clusterOptions = {
        " -A ${params.project} -p ${params.partition} "
    }
    scratch = true
    stageInMode = 'copy'
    stageOutMode = 'copy'

    //Resource and module requirements
    withName:
    FASTP {
        container = 'staphb/fastp:latest'
        cpus = 4
        time = 10.m
    }

    withName:
    SHOVILL {
        container = 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--hdfd78af_1'
        cpus = 4
        memory = 64.GB
        time = 90.m
    }

    withName:
    ASSEMBLY_STATS {
        container = 'staphb/bbtools:latest'
        cpus = 1
        time = 20.m
    }

    withName:
    CLASSIFY_TAXONOMY {
        container = 'staphb/kraken2:latest'
        cpus = 8
        memory = 200.GB
        time = 30.m
    }

    withName:
    PROKKA {
        container = 'staphb/prokka:1.14.5'
        //container = 'quay.io/biocontainers/prokka:1.14.6--pl526_0'
        cpus = 8
        memory = 64.GB
        time = 45.m
    }

    withName:
    MULTIQC {
        container = 'staphb/multiqc:latest'
        cpus = 1
        time = 30.m
    }
}

## Running
Run the pipeline in `screen` session, to avoid interrupting the workflow or use `-bg` when running `nextflow` [docs](https://www.nextflow.io/docs/latest/cli.html#execution-as-a-background-job).

# Load relevant modules
module load PDC/23.12 java/17.0.4 singularity anaconda3

# Folder to store the containers
export NXF_SINGULARITY_CACHEDIR=/cfs/klemming/projects/NXF_SINGULARITY_CACHEDIR
mkdir -P $NXF_SINGULARITY_CACHEDIR

nextflow -c containers.config run ctmrbio/BACTpipe \
  -with-singularity \
  --project uppmax.staff \
  --partition shared \
  --reads 'test_data/*_R{1,2}_001.fastq.gz' \
  --kraken2_db '/cfs/klemming/pdc/software/dardel/sw-uppmax/data/Kraken2_data/20240327-162424' \
  --keep_trimmed_fastq \
  --shovill_kmers 31,33,55,77


## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uu.se/en/centre/uppmax)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)

###### tags: `UPPMAX`, `PDC`