Template Pipeline Readme

Pipeline Name and Version

This pipeline performs the following tasks:

• Step 1 (using X program)
• Step 2 (using X program)

Download

Use git clone git clone [email protected]:HumanCellAtlas/skylab.git

Link to public methods repositories with this WDL

Requirements

Dockers

List dockers with location. Use versioned dockers and specify version

• eg: STAR v2_5_3a docker: humancellatlas/star_dev:v1

Genome Reference

Write down what is needed in the reference bundle for this pipeline, and a link to the WDL that reliably recreates it. Including which versions are used.

List out inputs below

• refFlat
• genome fasta
• interval list of rRNA

Example Input Data

Give information on the example test data in the input json example. Include:

• Where it came from (link to wdl to produce it)
• What it is
• How large it is
• Expected run time in this pipeline

Output Description

List of outputs from WDL and what they are

• Aligned.sortedByCoord.out.bam aligned output bam from STAR sorted by coordinate
• sample.alignment_summary_metrics quality metrics fromPicard CollectAlignmentSummaryMetrics

Limitations

List any known limitations of this pipeline