{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1344","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1344/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1344/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1344/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1344","id":149066609,"number":1344,"title":"Errors when using MultiQC: list passed instead of path","user":{"login":"lbeltrame","id":25192,"avatar_url":"https://avatars.githubusercontent.com/u/25192?v=3","gravatar_id":"","url":"https://api.github.com/users/lbeltrame","html_url":"https://github.com/lbeltrame","followers_url":"https://api.github.com/users/lbeltrame/followers","following_url":"https://api.github.com/users/lbeltrame/following{/other_user}","gists_url":"https://api.github.com/users/lbeltrame/gists{/gist_id}","starred_url":"https://api.github.com/users/lbeltrame/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbeltrame/subscriptions","organizations_url":"https://api.github.com/users/lbeltrame/orgs","repos_url":"https://api.github.com/users/lbeltrame/repos","events_url":"https://api.github.com/users/lbeltrame/events{/privacy}","received_events_url":"https://api.github.com/users/lbeltrame/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-18T07:27:20Z","updated_at":"2016-04-18T10:40:54Z","closed_at":"2016-04-18T10:40:54Z","body":"Master as of today:\r\n\r\n```python\r\nTraceback (most recent call last):\r\n  File \"/storage/rozo/bcbio/anaconda/bin/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/storage/rozo/bcbio/anaconda/bin/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 39, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 82, in _run_toplevel\r\n    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 184, in variant2pipeline\r\n    samples = qcsummary.generate_parallel(samples, run_parallel)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 48, in generate_parallel\r\n    samples = run_parallel(\"multiqc_summary\", [samples])\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 28, in run_parallel\r\n    return run_multicore(fn, items, config, parallel=parallel)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 86, in run_multicore\r\n    for data in joblib.Parallel(parallel[\"num_jobs\"])(joblib.delayed(fn)(x) for x in items):\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 804, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 662, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 570, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 183, in __init__\r\n    self.results = batch()\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 72, in __call__\r\n    return [func(*args, **kwargs) for func, args, kwargs in self.items]\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 143, in multiqc_summary\r\n    return qcsummary.multiqc_summary(*args)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 920, in multiqc_summary\r\n    folders.append(os.path.dirname(pfiles))\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/posixpath.py\", line 122, in dirname\r\n    i = p.rfind('/') + 1\r\nAttributeError: 'list' object has no attribute 'rfind'\r\n```\r\n\r\n`pfiles` is a list, and not a string."}}