New option: run fab fusion:manifest=manifest.tsv,base=treeshop (in place of fab process) to run fusion only on all samples in the manifest.
When bams are generated by the fusion pipeline, they will be placed in primary/derived rather than downstream/secondary.
implementation: breaks out code previously in process() into functions _fusions() (run fusion on one sample) and _setup() (sets up the fastq files for one sample). Then adds new function fusion() which runs only those steps.
issues: #17, #24
New option: run
fab fusion:manifest=manifest.tsv,base=treeshop(in place offab process) to run fusion only on all samples in the manifest.When bams are generated by the fusion pipeline, they will be placed in
primary/derivedrather thandownstream/secondary.implementation: breaks out code previously in process() into functions _fusions() (run fusion on one sample) and _setup() (sets up the fastq files for one sample). Then adds new function fusion() which runs only those steps.