from pyppl import PyPPL, Proc, Channel, params
params('prefix', '--param-')
params.datadir \
.setRequired() \
.setDesc('The data directory containing the data files.')
# or
# params.datadir.required = True
# params.datadir.desc = 'The data directory containing the data files.'
params = params.parse()
pSort = Proc(desc='Sort files.')
pSort.input = {"infile:file": Channel.fromPattern(params.datadir + '/*.txt')}
pSort.output = "outfile:file:{{in.infile | fn}}.sorted"
pSort.forks = 5
pSort.exdir = './export'
pSort.script = """
sort -k1r {{in.infile}} > {{out.outfile}}
"""
PyPPL().start(pSort).run()
from pyppl import PyPPL, Channel
# import predefined processes
from TCGAprocs import pBamToFastq, pAlignment, pBamSort, pBamMerge, pMarkDups
# Load the bam files
pBamToFastq.input = Channel.fromPattern('./data/*.bam')
# Align the reads to reference genome
pAlignment.depends = pBamToFastq
# Sort bam files
pBamSort.depends = pAlignment
# Merge bam files
pBamMerge.depends = pBamSort
# Mark duplicates
pMarkDups.depends = pBamMerge
# Export the results
pMarkDups.exdir = './export/realigned_Bams'
# Specify the start process and run the pipeline
PyPPL().start(pBamToFastq).flowchart().run({
'forks': 2,
'_log': {
'shorten': 40
}
})
from pathlib import Path
from pyppl import PyPPL, Proc, Channel
mockdir = Path(__file__).resolve().parent.parent.parent / 'tests' / 'mocks'
pSort = Proc(desc='Sort files.')
pSort.input = {"infile:file": Channel.fromPattern("./data/*.txt")}
pSort.output = "outfile:file:{{i.infile | fn}}.sorted"
# specify the runner
pSort.runner = 'sge'
# specify the runner options
# using mock sge commands
pSort.sgeRunner = {
"qsub": mockdir / 'qsub',
"qstat": mockdir / 'qstat',
"qdel": mockdir / 'qdel',
}
pSort.preCmd = 'rm -f %s' % (mockdir / 'sge.jobs.log') # clear the queue
pSort.forks = 5
pSort.exdir = './export'
pSort.script = """
sort -k1r {{i.infile}} > {{o.outfile}}
"""
PyPPL().start(pSort).run()
from os import path
from pyppl import PyPPL, Proc, Channel
from pyparam import params
def fn(fpath):
return path.basename(fpath).split('.')[0]
params.datadir.required = True
params.datadir.desc = 'The data directory containing the data files.'
params = params._parse()
pSort = Proc(desc='Sort files.')
pSort.input = {
"infile:file": Channel.fromPattern(params['datadir'] + '/*.txt')
}
pSort.output = "outfile:file:{{i.infile | fn}}.sorted"
pSort.forks = 5
pSort.exdir = './export'
pSort.envs.fn = fn
pSort.script = """
sort -k1r {{i.infile}} > {{o.outfile}}
"""
PyPPL().start(pSort).run()
