chapmanb/bcbio-nextgen — pull request #293 by mjafin (2014-02-06 11:42:15+00:00)
Title: Added support for tumor-only calling and use of normal_panel vcf in mute...

...ct.py

Hi Brad,
If you look at this pull request, it will run the cancer_devel test past mutect calling just fine, but then dies at a later stage because of missing 'normal' in the vcf I reckon. Error thread below:
```
[2014-02-06 11:41] multiprocessing: split_variants_by_sample
Traceback (most recent call last):
File "/home/klrl262/miniconda/envs/bcbio-test/bin/bcbio_nextgen.py", line 5, in
pkg_resources.run_script('bcbio-nextgen==0.7.7a', 'bcbio_nextgen.py')
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/pkg_resources.py", line 505, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/pkg_resources.py", line 1245, in run_script
execfile(script_filename, namespace, namespace)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/EGG-INFO/scripts/bcbio_nextgen.py", line 59, in
main(**kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/EGG-INFO/scripts/bcbio_nextgen.py", line 39, in main
run_main(**kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/pipeline/main.py", line 41, in run_main
fc_dir, run_info_yaml)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/pipeline/main.py", line 88, in _run_toplevel
for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items):
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/pipeline/main.py", line 311, in run
samples = region.parallel_variantcall_region(samples, run_parallel)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/pipeline/region.py", line 133, in parallel_variantcall_region
"vrn_file", ["region", "sam_ref", "config"])
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/distributed/split.py", line 36, in grouped_parallel_split_combine
ungrouped_output = parallel_fn(ungroup_name, grouped_output)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/distributed/multi.py", line 27, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/distributed/multi.py", line 81, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/joblib-0.8.0a3-py2.7.egg/joblib/parallel.py", line 644, in __call__
self.dispatch(function, args, kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/joblib-0.8.0a3-py2.7.egg/joblib/parallel.py", line 391, in dispatch
job = ImmediateApply(func, args, kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/joblib-0.8.0a3-py2.7.egg/joblib/parallel.py", line 129, in __init__
self.results = func(*args, **kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/utils.py", line 46, in wrapper
return apply(f, *args, **kwargs)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/distributed/multitasks.py", line 57, in split_variants_by_sample
return multi.split_variants_by_sample(*args)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/site-packages/bcbio_nextgen-0.7.7a-py2.7.egg/bcbio/variation/multi.py", line 60, in split_variants_by_sample
assert vcfutils.get_paired_phenotype(data["group_orig"][0][0]) == "normal"
AssertionError
ERROR

======================================================================
ERROR: Test cancer calling without normal samples or with normal VCF panels.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/klrl262/dev/bcbio-nextgen/tests/test_automated_analysis.py", line 283, in test_7_cancer_nonormal
subprocess.check_call(cl)
File "/home/klrl262/miniconda/envs/bcbio-test/lib/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['bcbio_nextgen.py', '/home/klrl262/dev/bcbio-nextgen/tests/data/automated/post_process-sample.yaml', '/home/klrl262/dev/bcbio-nextgen/tests/data/automated/run_info-cancer2.yaml']' returned non-zero exit status 1

----------------------------------------------------------------------
Ran 1 test in 29.398s
```