bmpvieira on master
Refactor to add CLI 3.0.0 (compare)
bmpvieira on master
Refactor to add CLI 3.0.0 (compare)
dependabot[bot] on npm_and_yarn
Bump bl from 1.2.2 to 4.0.3 Bu… (compare)
dependabot[bot] on npm_and_yarn
Bump bl from 1.2.2 to 4.0.3 Bu… (compare)
bmpvieira on master
Hyperlink DOIs to preferred res… Merge pull request #5 from katr… (compare)
bmpvieira on master
Hyperlink DOIs to preferred res… Merge pull request #5 from katr… (compare)
bionode-fasta
only serialises the data to JSON if you use it in Object mode (i.e., fasta.obj(), please see https://github.com/bionode/bionode-fasta#usage)
npm run build-browser
inside bionode-fasta
git repository, it should generate a bionode-fasta.min.js
that you can use browser side
fasta-parser
is off the top of your head?
dev
branch. However, bionode-watermill might be hard for beginners, but if you want to give it a try... we are here to help.
task
for user to declare what their operationCreator
returns)
One cool thing to do would be to use ES6 template literals to do something like
const { task, python } = require('bionode-watermill')
const mytask = task({
input: '*.txt',
output: '*.foo',
name: 'My task'
}, ({ input }) => python`
with open('output.foo') as output:
with open('${input}') as input:
for line in input:
output.write(line.upper())
`)
// where `python` returns something like
// { language: 'python', executer: '/usr/bin/env python3', code }
// watermill writes the script, marks it executable, stores it in task dir
then it would be frictionless to experiment with quick scripts in a bunch of languages, write small simple scripts for visualization with R, etc. using ${variable
in source code for a script is kinda sketchy but maybe OK for quick experimentaion. Nextflow has something similar for scripts in any language (you just put #!/usr/bin/env python3
at top)
OR maybe that program should go under a prop
of the task, so it is called as a CLI like usual
operationCreator
is the second paramater passed to task
, the first is the object props
bionode-ncbi download sra PRJNA183192
repeats the first SRA file, SRR629557.sra
until infinity
bionode-ncbi download
is very verbose by default (to pipe into other tools)
bionode-ncbi download sra --pretty PRJNA183192
to display a progress bar instead
jq
installed: bionode-ncbi urls sra PRJNA183192 | sed 's|.*url":"\(.*\)","uid.*|\1|' | xargs wget