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'.

Test the config file

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

mamba activate nextflow

# 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,sasquatch \
    --outdir "/home/$USER/temp/nf-core-rnaseq-test" \
    --assoc "rsc" \
    --validationSchemaIgnoreParams 'assoc'

nextflow run -c 'conf/seattlechildrens.config' \
    nf-core/fetchngs \
    -r 1.12.0 \
    -profile test,sasquatch \
    --input ./ids.csv \
    --download_method 'sratools' \
    --assoc "rsc" \
    --outdir "/home/$USER/fetchngs"

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

Change log

2025.02.21 Preliminary updates for Sasquatch. 2023.03.18 Built during nf-core biohackathon which synced for Cybertron and PBS.