code from 03-27-25
# create a screen session
screen -S nextflow
# request a compute node (mem and time requests can be modified)
salloc -A srlab -p cpu-g2-mem2x -N 1 -c 1 --mem=16GB --time=12:00:00
# load the nextflow environment
apptainer shell --bind /usr/bin/ /gscratch/ /gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-a83e518.sif
nextflow run \
nf-core/fetchngs \
-resume \
-c /gscratch/srlab/nextflow/uw_hyak_srlab.config \
--input /gscratch/scrubbed/strigg/analyses/20250327_FetchNGS/ids.csv \
--outdir /gscratch/scrubbed/strigg/analyses/20250327_FetchNGS \
--download_method sratools
installed miniforge in nextflow bin
/gscratch/srlab/nextflow/bin/miniforge/bin/mamba create -p miniforge/envs/nextflow -c bioconda -c conda-forge python=3.8 nf-core nextflow -y -q
/gscratch/srlab/nextflow/bin/miniforge/bin/mamba init
#activate srlab nextflow env
/gscratch/srlab/nextflow/bin/miniforge/bin/mamba activate /gscratch/srlab/nextflow/bin/miniforge/envs/nextflow
#variables don't seem set an i don't know where NXF_HOME or NXF_TEMP are. so I'll just run the pipeline and see what happens
NXF_HOME='/gscratch/srlab/programs/nextflow'
If you don’t have mamba in your path, run
/gscratch/srlab/nextflow/bin/miniforge/bin/mamba init
then
source ~/.bashrc
create a screen session
screen -S nextflow
request a compute node (mem and time requests can be modified)
salloc -A srlab -p cpu-g2-mem2x -N 1 -c 1 –mem=16GB –time=12:00:00
nextflow run nf-core/fetchngs -resume -c /gscratch/srlab/nextflow/uw_hyak_srlab.config –input /gscratch/scrubbed/strigg/analyses/20250327_FetchNGS/ids.csv –outdir output –download_method sratools
load the nextflow environment
#apptainer shell –bind /gscratch/ srlab-R4.4-bioinformatics-container-0751826.sif
run nextflow pipeline
nextflow run
nf-core/