nextflow_scri_config

An SCRI nextflow profile for NF-Core for reference which is pulled to 'https://github.com/nf-core/configs/blob/master/conf/seattlechildrens.config'.

The provided config here does not include the singularity scope, but SCRI does have some recommended settings for Singularity in the nextflow config, but might not be correct for all pipelines.

Here is an example of the singularity scope settings used in most SCRI pipelines.

//Configs for singularity containers on cybertron
singularity {
    autoMounts = true
    cacheDir = "$HOME/singularity_test"
    runOptions = '--containall --no-home'
}

Test the config file

Please note that --project parameter can be specified on the command line in nextflow run or in the seattlechildrens.config.

ml singularity

# For running on an interactive session on cybertron with singularity module loaded
nextflow run -c 'conf/seattlechildrens.config' \
    nf-core/rnaseq \
    -r 3.14.0 \
    -profile test,local_singularity \
    --outdir "/home/$USER/temp/nf-core-rnaseq-test" \
    --project "207f23bf-acb6-4835-8bfe-142436acb58c" \
    --validationSchemaIgnoreParams 'queue,project'

# For executing the jobs on the HPC cluster with singularity containers
# doesn't work due to bioconductor-dupradar:1.28.0--r42hdfd78af_0
nextflow run -c 'conf/seattlechildrens.config' \
    nf-core/rnaseq \
    -r 3.14.0 \
    -profile test,PBS_singularity \
    --max_memory 32.GB \
    --outdir "/home/$USER/temp/nf-core-rnaseq-test" \
    --project "207f23bf-acb6-4835-8bfe-142436acb58c" \
    --validationSchemaIgnoreParams 'queue,project'

nextflow run -c 'conf/seattlechildrens.config' \
    nf-core/fetchngs \
    -r 1.12.0 \
    -profile test,PBS_singularity \
    --input ./ids.csv \
    --download_method 'sratools' \
    --project "207f23bf-acb6-4835-8bfe-142436acb58c" \
    --outdir "/home/$USER/fetchngs"

nf-core launch nf-core/methylseq -r 2.6.0

Change log

2023.03.18 Built during nf-core biohackathon which synced for Cybertron and PBS.