nf-diffbind

Create the test directory:

mkdir -p /tmp/nextflow_atac_local_test/macs_test

Download the demo data:

cd /tmp/nextflow_atac_local_test/macs_test/
curl -J -O https://datashare.mpcdf.mpg.de/s/nzO5RFUXK3kyhuw/download
unzip bowtie2_output.zip 
curl -J -O https://datashare.mpcdf.mpg.de/s/9ZCprbdEHWoL5vL/download
unzip macs2_output.zip 

Download the paramaters file:

cd /tmp/nextflow_atac_local_test/macs_test/
PARAMS=params.local.json
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nf-diffbind/main/${PARAMS}
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nf-diffbind/main/sample_sheet.xlsx

Get the latest repo:

cd /tmp/nextflow_atac_local_test/
git clone https://github.com/mpg-age-bioinformatics/nf-diffbind.git
git clone https://github.com/mpg-age-bioinformatics/nf-CHIPseeker.git

Run the workflow:

nextflow run nf-diffbind -params-file  macs_test/${PARAMS} -entry images --user "$(id -u):$(id -g)" && \
nextflow run nf-diffbind -params-file  macs_test/${PARAMS} -entry samplesheet --user "$(id -u):$(id -g)" && \
nextflow run nf-diffbind -params-file  macs_test/${PARAMS} --user "$(id -u):$(id -g)"

For annotating the peaks

nextflow run nf-CHIPseeker -params-file ./nf-CHIPseeker/params.local.json -entry images --user "$(id -u):$(id -g)" && \
nextflow run nf-CHIPseeker -params-file ./nf-CHIPseeker/params.local.json --user "$(id -u):$(id -g)" 

Contributing

Make a commit, check the last tag, add a new one, push it and make a release:

git add -A . && git commit -m "<message>" && git push
git describe --abbrev=0 --tags
git tag -e -a <tag> HEAD
git push origin --tags
gh release create <tag>