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 a params or config file.

mamba activate nextflow

export ASSOC="rsc"

# For running on an interactive session on sasquatch
nextflow run \
    nf-core/rnaseq \
    -r 3.14.0 \
    -profile seattlechildrens,test \
    --outdir "/data/hps/assoc/private/rsc/user/$USER/nf-core-rnaseq-test" \
    -workDir "/data/hps/assoc/private/rsc/user/$USER/nf-core-rnaseq-test-temp"

export ASSOC="rsc"

nextflow run \
    nf-core/fetchngs \
    -r 1.12.0 \
    -profile seattlechildrens,test \
    --input ./ids.csv \
    --download_method 'sratools' \
    --outdir "/data/hps/assoc/private/rsc/user/$USER/fetchngs-test" \
    -workDir "/data/hps/assoc/private/rsc/user/$USER/fetchngs-test-temp"

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.