Julian Mazzitelli
Julian Mazzitelli
Due to the way we [parse a string into a child process](https://github.com/bionode/bionode-watermill/blob/46499966a41c5977941ba4b617298aa64192b2c3/lib/utils/shell.js#L12) it may be the case that certain operations (e.g., a bash for/while read loop) may not run. It...
In order to be a *streaming* workflow engine, we need to support the ability to `pipe` between tasks. This does not add much to the "traditional" pipeline which mostly reads/writes...
Todos: - [ ] keep stdout/stderr logs in main logs? - [ ] set absolute path to `stdout.txt` and `stderr.txt` in task state - [ ] how to handle this...
This means to be able to pass a custom file validator on a per task basis, something like: ```javascript const mytask = task({ input: '*.sra', output: '*.vcf' validators: (file) =>...
write a test for a simple task that uses a through2 transform stream (to convert lowercase to uppercase for example) later perhaps same test can be used to check if...
- [ ] `join(A, B, C)`, `C` fails, run again - [ ] `join(A, B, C)`, `A`'s params change, hash of output of A changes, so B should rerun (instead...
Would be super simple, essentially wrap a module into `(x, f) => f(x)` where `f(x)` is `true` or `f(x)` is `false`. `x` can then be something like ``` javascript require('is-my-schema-valid')({...
- parallelization with patches of bam - for example, split bam into 20 sections if 20 cores available - both options: **concatenate** vs. **run analysis on regions** Example: - get...
```javascript // We want to run a bunch of variant callers // Then count common SNPs const variantCallerInput = { reference: '*_genomic.fna', bam: '*.bam', _bai: '*.bam.bai' } // two tasks...