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A Software Workflow Management System Based on DoIt

Project description

JUDI - Bioinformatics Pipeline: Just Do It

judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings.

Sample Code

Snippet from tutorial, save it as

from judi import File, Task, add_param, combine_csvs

add_param('100 101 102 103'.split(), 'sample')
add_param('1 2'.split(), 'group')

REF = 'hg_refs/hg19.fa'
path_gen = lambda x: '{}_{}.fq'.format(x['sample'],x['group'])

class AlignFastq(Task):
  inputs = {'reads': File('orig_fastq', path = path_gen)}
  targets = {'sai': File('aln.sai')}
  actions = [('bwa aln {} {} > {}', [REF,'$reads','$sai'])]

class CreateBam(Task):
  mask = ['group']
  inputs = {'reads': AlignFastq.inputs['reads'],
             'sai': AlignFastq.targets['sai']}
  targets = {'bam': File('aln.bam', mask = mask)}
  actions = [('bwa sampe {} {} {} | samtools view -Sbh - | samtools sort - > {}', [REF,'$sai','$reads','$bam'])]

class GetCoverage(Task):
  mask = ['group']
  inputs = {'bam': CreateBam.targets['bam']}
  targets = {'cov': File('cov.csv', mask = mask)}
  actions = [('(echo val; samtools rmdup {} - | samtools mpileup - | cut -f4) > {}', ['$bam','$cov'])]

class CombineCoverage(Task):
  mask = ['group', 'sample']
  inputs = {'cov': GetCoverage.targets['cov']}
  targets = {'csv': File('combined.csv', mask = mask),
             'pdf': File('pltcov.pdf', mask = mask, root = '.')}
  actions = [(combine_csvs, ['#cov', '#csv']),
             ("""echo "library(ggplot2); pdf('{}')
              ggplot(read.csv('{}'), aes(x = val)) +
              geom_density(aes(color = factor(sample)))"\
              | R --vanilla""", ['$pdf','$csv'])]

Run from terminal:

$ doit list
$ doit
. AlignFastq:group~1,sample~100
. AlignFastq:group~2,sample~100
. AlignFastq:group~1,sample~101
. AlignFastq:group~2,sample~101
. AlignFastq:group~1,sample~102
. AlignFastq:group~2,sample~102
. AlignFastq:group~1,sample~103
. AlignFastq:group~2,sample~103
. CreateBam:sample~100
. CreateBam:sample~102
. CreateBam:sample~103
. CreateBam:sample~101
. GetCoverage:sample~100
. GetCoverage:sample~102
. GetCoverage:sample~103
. GetCoverage:sample~101
. CombineCoverage:

Project Details


The MIT License Copyright (c) 2019-2020 Soumitra Pal

see LICENSE file


judi is tested on python 3.6.

$ pip install judi


  • doit


docs folder contains ReST documentation based on Sphinx.

$ make html


On github create pull requests using a named feature branch.

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