# the License.
"""
Provide wrappers for tasks related to fastq files.
Classes
-------
"""
import os
import luigi
import ratatosk.lib.files.external
from ratatosk.job import JobTask
from ratatosk.log import get_logger
logger = get_logger()
class FastqFileLink(JobTask):
outdir = luigi.Parameter(default=os.curdir)
# This is tricky: it is easy enough to make links based on
# absolute file names. The problem is that the information about
# the original path is lost in successive tasks, so that a task
# that takes as input a bam file in the current directory will not
# know where the link came from; hence, we need an indir parameter
# for downstream tasks.
indir = luigi.Parameter(default=os.curdir)
parent_task = luigi.Parameter(default=("ratatosk.lib.files.external.FastqFile", ), is_list=True)
suffix = luigi.Parameter(default=("",), is_list=True)
def requires(self):
cls = self.parent()[0]
Classes
-------
"""
import os
import luigi
import logging
import ratatosk.lib.files.input
from ratatosk.utils import rreplace, fullclassname
from ratatosk.job import JobTask, JobWrapperTask
from ratatosk.jobrunner import DefaultShellJobRunner
from ratatosk.log import get_logger
import ratatosk.shell as shell
logger = get_logger()
class InputVcfFile(ratatosk.lib.files.input.InputVcfFile):
pass
class snpEffJobRunner(DefaultShellJobRunner):
def _make_arglist(self, job):
if not job.jar() or not os.path.exists(
os.path.join(job.path(), job.jar())):
logger.error("Can't find jar: {0}, full path {1}".format(
job.jar(), os.path.abspath(job.jar())))
raise Exception("job jar does not exist")
arglist = [job.java()] + job.java_opt() + [
'-jar', os.path.join(job.path(), job.jar())
