Examples

• Example Commands
• Example Config
• Distributed Run

Example Commands

Run sample(s) locally using the manifest

1. toil-rnaseq generate
2. Fill in config and manifest
3. toil-rnaseq run ./example-jobstore

Toil options can be appended to toil-rnaseq run, for example: toil-rnaseq run ./example-jobstore --retryCount=1 --workDir=/data

For a complete list of Toil options, just type toil-rnaseq run -h

Run a variety of samples locally

1. toil-rnaseq generate-config
2. Fill in config
3. toil-rnaseq run ./example-jobstore --retryCount=1 --workDir=/data --samples \ s3://example-bucket/sample_1.tar file:///full/path/to/sample_2.tar https://sample-depot.com/sample_3.tar

Example Config

star-index: s3://cgl-pipeline-inputs/rnaseq_cgl/ci/starIndex_chr6.tar.gz
kallisto-index: s3://cgl-pipeline-inputs/rnaseq_cgl/kallisto_hg38.idx
rsem-ref: s3://cgl-pipeline-inputs/rnaseq_cgl/ci/rsem_ref_chr6.tar.gz
output-dir: /data/my-toil-run
cutadapt: true
fastqc: true
bamqc:
fwd-3pr-adapter: AGATCGGAAGAG
rev-3pr-adapter: AGATCGGAAGAG
ssec:
wiggle:
save-star-bam:
save-hera-bam:
gdc-token:
ci-test:

Example with local input files

star-index: file://data/starIndex_chr6.tar.gz
kallisto-index: file://data/kallisto_hg38.idx
rsem-ref: file://data/rsem_ref_chr6.tar.gz
output-dir: /data/my-toil-run
cutadapt: true
fastqc: true
bamqc:
fwd-3pr-adapter: AGATCGGAAGAG
rev-3pr-adapter: AGATCGGAAGAG
ssec:
wiggle:
save-star-bam:
save-hera-bam:
gdc-token:
ci-test:

Distributed Run

See the Toil documentation: Launching a Toil Workflow in AWS and the example in the wiki here.