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Makefile to run the expression, fusion and variant secondary pipelines used by Treehouse on a single machine from the command line.

Requirements

Docker 1.12.x
16+ cores
50G+ memory
100G+ storage for reference files
100G+ storage per sample

Getting Started

Clone this repository. Then, to validate it on provided TEST fastq files, run 'make'.

git clone https://github.com/UCSC-Treehouse/pipelines.git
cd pipelines

make

References will be downloaded, verified via MD5, and then the included TEST paired fastqs will be run through the pipelines and outputs verified. This will take approximately 20-30 minutes on a 16 core machine excluding reference file download time. At the end you should see:

Verifying md5 of output of TEST file
tar -xOzvf outputs/expression/TEST_R1merged.tar.gz FAIL.TEST_R1merged/RSEM/rsem_genes.results |
md5sum -c md5/expression.md5
FAIL.TEST_R1merged/RSEM/rsem_genes.results
-: OK
cut -f 1 outputs/fusions/star-fusion-non-filtered.final | sort | md5sum -c md5/fusions.md5
-: OK
tail -n 10 outputs/variants/mini.ann.vcf | md5sum -c md5/variants.md5
-: OK

NOTE: Fail is expected as the test file contains too few reads to pass our qc

Under outputs you should see the following:

outputs/
├── expression
│   ├── TEST_R1merged.sortedByCoord.md.bam
│   └── TEST_R1merged.tar.gz
├── fusions
│   ├── Log.final.out
│   ├── star-fusion-gene-list-filtered.final
│   └── star-fusion-non-filtered.final
├── qc
│   ├── bam_umend_qc.json
│   ├── bam_umend_qc.tsv
│   └── readDist.txt
└── variants
    └── mini.ann.vcf

Replace the TEST files under samples/ with your own pair of fastq's with _1/_2 or _R1/_R2 in their name and then:

make expression qc fusions variants

A typical single sample running all three pipelines will take about 18 hours depending on the size/depth. Of this around 8 hours is expression, 1.5 hours is qc, 2 hours is fusion and a few minutes for variants.

Expression Outputs

The output is a tar.gz file with a variety of results merged.

TEST_R1merged/RSEM/rsem_genes.results
TEST_R1merged/RSEM/rsem_isoforms.results
TEST_R1merged/RSEM/Hugo/rsem_genes.hugo.results
TEST_R1merged/RSEM/Hugo/rsem_isoforms.hugo.results
TEST_R1merged/Kallisto/run_info.json
TEST_R1merged/Kallisto/abundance.tsv
TEST_R1merged/Kallisto/abundance.h5
TEST_R1merged/QC/fastQC/R1_fastqc.html
TEST_R1merged/QC/fastQC/R1_fastqc.zip
TEST_R1merged/QC/fastQC/R2_fastqc.html
TEST_R1merged/QC/fastQC/R2_fastqc.zip
TEST_R1merged/QC/STAR/Log.final.out
TEST_R1merged/QC/STAR/SJ.out.tab

Pipeline Sources

For additional information and source code for each pipeline see the following github repos:

[https://github.com/BD2KGenomics/toil-rnaseq]

[https://github.com/UCSC-Treehouse/bam-umend-qc]

[https://github.com/UCSC-Treehouse/fusion]

[https://github.com/UCSC-Treehouse/mini-var-call]

For specific parameters and versions used in this pipeline, see the Pipelines Versions document.

Treehouse Internal Use

See the Treeshop document for running on VMs via docker-machine and fabric.

Security Note:

This pipeline runs a docker of the mend_qc tool which has a vulnerability in the numpy version used (1.13.3). However this is not expected to be a problem in the context of the mend_qc docker.