An SCRI nextflow profile for NF-Core for reference which is pulled to 'https://github.com/nf-core/configs/blob/master/conf/seattlechildrens.config'.
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
2025.02.21
Preliminary updates for Sasquatch.
2023.03.18
Built during nf-core biohackathon which synced for Cybertron and PBS.