# STQ at PDC

https://github.com/TheJacksonLaboratory/STQ

## Preparing the pipeline

:::danger
!!! WARNING !!!
Seems that the GPU accelerated containers are setup with CUDA i.e. NVIDIA GPU support, which will not work on Dardel !!! [Hardware info - Dardel](https://www.pdc.kth.se/hpc-services/computing-systems/dardel-hpc-system/about-the-dardel-system-1.1053338)
To switch off the GPU mode, one needs to add
`params.hovernet_device_mode = cpu` in `nextflow.config` in the corresponding section...
:::

> preliminary draft instructions

module load PDC nextflow apptainer
export APPTAINER_DISABLE_CACHE=true

# Somewhere in your project space
cd my-piepline-run
git clone https://github.com/TheJacksonLaboratory/STQ.git

# Pull the containers
singularity pull docker://quay.io/jaxcompsci/xenome:1.0.1
...

# deal with " conf/containers.config"
# note add the template at the bottom, since it is incomplette.
# well - there are more fixes needed...

`run.sh`

workflow="deconvolution_indices" ### "two_references" "one_reference" "arbitrary_grid" "deconvolution_indices"
samplesheet="./assets/samplesheet_demo.csv"
workdir="./work_test"
outdir="./results_test"
binddir="/cfs/klemming"

#----------------------------------------------------------------------------------------------------

./check.sh

SLURM_SUBMIT_DIR=`pwd`

sbatch \
submit.sb $workflow "$samplesheet" "$workdir" "$outdir" "$binddir"

`submit.sb`

#!/bin/bash --login
#SBATCH -A naiss2025-22-385
#SBATCH -p shared
#SBATCH -t 3-00:00:00
#SBATCH -J deconvolution
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=[e-mail]
#SBATCH --mem=56G
#SBATCH --ntasks=1

module load PDC nextflow apptainer

cd $SLURM_SUBMIT_DIR

nextflow run main.nf \
-w $3 \
-profile slurm,singularity \
-resume \
--input=$2 \
--outdir=$4 \
--workflow=$1 \
--bind="-B $5"

### `nextcloud.config`
- still testing, please make these changes

...
process {
    resourceLimits = [ cpus: 256, memory: 1790.GB, time: 7.d ]
    // beforeScript   = 'module load PDC apptainer'

...

profiles {
    slurm {
        executor {
            name = "slurm"
            submitRateLimit = '1/1s'
            queueSize = 20
            exitReadTimeout = '600s'
            //pollInterval = '30s'
        }
        process.queue = "shared -A naiss2025-22-385"
        process.clusterOptions = ''
        process.module = "slurm"
    }
    singularity {
        process.module = 'PDC:apptainer'          
        singularity.enabled    = true             
        singularity.envWhitelist = 'CUDA_VISIBLE_DEVICES'
        singularity.autoMounts = true             
        docker.enabled         = false            
        podman.enabled         = false            
        shifter.enabled        = false            
        charliecloud.enabled   = false            
        singularity.runOptions = "-B /cfs/klemming " + params.bind                                                                                               
    }   

### `conf/containers.config`

params {                                                  
                                                          
    container_dir              = "/cfs/klemming/scratch/p/pmitev/RT-202508.25-317850-STQ/STQ/containers"
                                                          
    container_inception        = "${params.container_dir}/container-mamba-inception.sif"
    container_hovernet         = "${params.container_dir}/local/container-singularity-hovernet-py.sif"
    container_stainnet         = "${params.container_dir}/container-singularity-stainnet.sif"
    container_staintools       = "${params.container_dir}/container-singularity-staintools.sif"
    container_vips             = "${params.container_dir}/container-singularity-vips.sif"
                                                          
    container_uni_conch       = "${params.container_dir}/hf-uni-conch.sif"
    container_ctranspath       = "${params.container_dir}/local/mamba-timm.sif"
    container_deepfocus        = "${params.container_dir}/deepfocus.sif"
    container_ome              = "${params.container_dir}/local/ome.sif"
                                                          
    container_xenome           = "/projects/compsci/omics_share/meta/containers/quay.io-jaxcompsci-xenome-1.0.1.img"
                                                          
    container_xengsort         = "${params.container_dir}/local/mamba-xenomake.sif"
    container_fastqtools       = "${params.container_dir}/container-singularity-fastqtools.sif"
    container_spaceranger      = "${params.container_dir}/container-singularity-spaceranger.sif"
                                                          
container_bafextract       = "${params.container_dir}/bafextract_v1.0.0.sif"                                                               
    container_samtools         = "${params.container_bafextract}"
                                                          
    container_velocyto         = "${params.container_dir}/container-singularity-velocyto.sif"
                                                          
                                                          
container_inception        = "${params.container_dir}/inception_v1.0.0.sif"
container_hovernet         = "${params.container_dir}/hovernet_v2.0.0.sif"
container_stainnet         = "${params.container_dir}/stainnet_v1.0.0.sif"
container_staintools       = "${params.container_dir}/staintools_v1.0.0.sif"
container_vips             = "${params.container_dir}/vips_v1.0.0.sif"
container_xenome           = "${params.container_dir}/xenome_v1.0.1.sif"
container_xengsort         = "${params.container_dir}/xenomake_v1.0.0.sif"
container_fastqtools       = "${params.container_dir}/fastqtools_v1.0.0.sif"
container_spaceranger      = "${params.container_dir}/spaceranger_v1.0.0.sif"
container_bafextract       = "${params.container_dir}/bafextract_v1.0.0.sif"
container_python           = "${params.container_dir}/pythonlow_v1.0.0.sif"
container_velocyto         = "${params.container_dir}/velocyto_v1.0.0.sif"
container_deepfocus        = "${params.container_dir}/deepfocus_v1.0.0.sif"
container_ome              = "${params.container_dir}/ome_v1.0.0.sif"
container_timm             = "${params.container_dir}/timm_v1.0.0.sif"
container_conch            = "${params.container_dir}/hfconch_v1.0.0.sif"
container_uni_conch        = "${params.container_dir}/hfconch_v1.0.0.sif"                                               
}

## 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: `PDC`, `Dardel`, `nextflow`, `RT317850`