This workflow is based on the following nextflow pipes:
- https://github.com/mpg-age-bioinformatics/nf-fastqc
- https://github.com/mpg-age-bioinformatics/nf-flexbar
- https://github.com/mpg-age-bioinformatics/nf-kallisto
- https://github.com/mpg-age-bioinformatics/nf-bowtie2
- https://github.com/mpg-age-bioinformatics/nf-macs
- https://github.com/mpg-age-bioinformatics/nf-diffbind
- https://github.com/mpg-age-bioinformatics/nf-CHIPseeker
- https://github.com/mpg-age-bioinformatics/nf-bedGraphToBigWig
- https://github.com/mpg-age-bioinformatics/nf-ATACseqQC
Create the test directory:
mkdir -p /tmp/nextflow_atac_local_complete_test
Download the demo data:
cd /tmp/nextflow_atac_local_complete_test
curl -J -O https://datashare.mpcdf.mpg.de/s/PcBd0kCPH7k82Z4/download
unzip raw_data.zip
Add the run script, paramaters file, and sample sheet to the project folder:
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nextflow-ATACSeq/main/params.local.json
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nextflow-ATACSeq/main/nextflow-ATACseq.local.sh
curl -J -O https://datashare.mpcdf.mpg.de/s/dUUKTLWHjYvNYh1/download
Run the local test:
bash nextflow-ATACseq.local.sh clone params.local.json
Once run is complete you will find in the work folder the file software.txt with information on all the respective versions used for your run.
Most relevant results files will be found in /tmp/nextflow_atac_local_complete_test/summary eg.:
./multiqc_out/multiqc_report.html
./bigwig_output/Hetero_TFAM_IgG.Rep_1_treat_pileup.bw
./bigwig_output/Hetero_TFAM_cGAS.Rep_1_treat_pileup.bw
./bigwig_output/WT_MEF_IgG.Rep_1_treat_pileup.bw
./bigwig_output/WT_MEF_cGAS.Rep_1_treat_pileup.bw
./bigwig_output/WT_TFAM_IgG.Rep_1_treat_pileup.bw
./bigwig_output/WT_TFAM_cGAS.Rep_1_treat_pileup.bw
./bigwig_output/YKO_MEF_IgG.Rep_1_treat_pileup.bw
./bigwig_output/YKO_MEF_cGAS.Rep_1_treat_pileup.bw
./diffbind3_output/annotated_master_table.xlsx
./diffbind3_output/consensus_peaks.xlsx
./diffbind3_output/general_QC.pdf
If you have a json file generated by flaski.
LATEST_RELEASE=$( curl --silent "https://api.github.com/repos/mpg-age-bioinformatics/nf-flaski-configs/releases/latest" | grep '"tag_name":' | sed -E 's/.*"([^"]+)".*/\1/' )
nextflow run mpg-age-bioinformatics/nf-flaski-configs -r ${LATEST_RELEASE} --raw /path/to/raw/data/folder --json /path/to/flaski/file.json --out /path/to/output/folder -profile local
curl -J -O https://raw.githubusercontent.com/mpg-age-bioinformatics/nextflow-rnaseq/main/nextflow-ATACSeq.local.sh
bash nextflow-ATACseq.local.sh clone /path/to/output/folder/params.json