Microtest is a repository of small test data from various data types, for testing pipelines.

(please include here a short description of any data files you add)

• atac-seq_PE.bam: Random sample of paired-end ATAC-seq
• atac-seq_SE.bam: Random sample of single-end ATAC-seq
• bs_aln_k1k3.bam: Bisulfite data aligned to the methylated/unmethylated spike-in control sequences (k1/k3).
• chip-seq_PE.bam: Random sample of paired-end ChIP-seq
• chip-seq_SE.bam: Random sample of single-end ChIP-seq
• chipmentation_PE.bam: Random sample of paired-end ChIPmentation
• chipmentation_SE.bam: Random sample of single-end ChIPmentation
• dropseq_human.bam: Random sample of Drop-seq from human
• dropseq_mouse.bam: Random sample of Drop-seq from mouse
• hichip_PE.bam: Random sample of paired-end Hi-ChIP
• wgbs1.bam/wgbs2.bam: Random samples of unaligned WGBS data.

# create and activate a virtual environment virtualenv microtestenv; cd microtestenv; . ./bin/activate # install the stack pip install "peppy>=0.30.2,<1.0.0" "looper>=1.2.0,<2.0.0" "piper>=0.12.1,<1.0.0" # clone open_pipelines and microtest git clone https://github.com/epigen/open_pipelines git clone https://github.com/epigen/microtest # run export CODE=`pwd` # run only tutorial pipeline (no additional dependecies) looper run microtest/config/microtest_config.yaml --sel-attr protocol --sel-incl Amplicon # or run all (would require additional software dependecies) # for now only ATAC-seq has been adapted looper run microtest/config/microtest_config.yaml --sel-attr protocol --sel-incl ATAC-seq

AMPLICON=`sed 's/,/\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 14` GUIDE=`sed 's/,/\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 15` python \	open_pipelines/pipelines/amplicon_simple.py \	-S microtest_amplicon \	-i microtest/data/amplicon.fastq.gz \	-g $GUIDE \	-a $AMPLICON \	-O microtest_amplicon

How samples were made:

samtools view -s .0001 sample.bam -b > new_sample.bam

1. Open a listening port for webhooks:
   1. Get ngrok at https://ngrok.com and open a port: ./ngrok 3456
   2. add that URL + "/payload" to the github webhook with a secret key
2. Create a listening server:
   1. git clone git@github.com:afrendeiro/github-webhook-handler.git
   2. modify github-webhook-handler/repos.json with your repositories that should trigger the testing and the secret key(s)
   3. start the server and leave it running: python github-webhook-handler/index.py 4567

When there is a push to your repositories, run_microtest.sh will run. This creates an isolated virtual environment, installs dependencies (not pipeline-specific ones though!) and runs the pipelines on the microtest data (similar to the example above).