run_differential_expression_demo-singularity.sh

#!/bin/sh

# check nextflow is in PATH
nextflow -version

# check singularity is in PATH
singularity --version

# create and use local temporary directory
export TMPDIR="$(pwd)/tmp"
mkdir -p ${TMPDIR}
export SINGULARITY_TMPDIR=${TMPDIR}
export SINGULARITY_CACHEDIR=${TMPDIR}
export NXF_SINGULARITY_CACHEDIR=${TMPDIR}
export SINGULARITY_LOCALCACHEDIR=${TMPDIR}

# Nextflow settings - one may need to set these
# export JAVA_HOME="/path/to/java/jre1.8.0_251"
# export JAVA_CMD="/path/to/java/jre1.8.0_251/bin/java"
# export NXF_OPTS="-Xms25G -Xmx25G"

# Run the DGE model demo
nextflow run \
    ../main.nf \
    -profile "local_singularity" \
    --file_anndata "$(pwd)/demo_data.h5ad" \
    --output_dir "$(pwd)/results" \
    -params-file "$(pwd)/params-dge_test_type_demo.yml" \
    -resume

# Run the GO and GSEA demo
nextflow run \
    ../main.nf \
    -profile "local_singularity" \
    --file_anndata "$(pwd)/demo_data.h5ad" \
    --output_dir "$(pwd)/results" \
    -params-file "$(pwd)/params-gsea_go_demo.yml" \
    -resume