{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/qiita/pulls/comments/32685245","id":32685245,"diff_hunk":"@@ -158,13 +184,70 @@ def _get_preprocess_fastq_cmd(raw_data, prep_template, params):\n     forward_seqs = sorted(forward_seqs)\n     reverse_seqs = sorted(reverse_seqs)\n     barcode_fps = sorted(barcode_fps)\n-    mapping_fps = sorted(mapping_fps)\n \n-    # Create the split_libraries_fastq.py command\n-    cmd = str(\"split_libraries_fastq.py --store_demultiplexed_fastq -i %s -b \"\n-              \"%s -m %s -o %s %s\"\n-              % (','.join(forward_seqs), ','.join(barcode_fps),\n-                 ','.join(mapping_fps), output_dir, params_str))\n+    # Create a temporary directory to store the split libraries output\n+    output_dir = mkdtemp(\n+        dir=qiita_config.working_dir,\n+        prefix='slq_out_%d_%d_' % (prep_template.id, raw_data.id))\n+\n+    # Add any other parameter needed to split libraries fastq\n+    params_str = params.to_str()\n+\n+    if len(forward_seqs) == 0:\n+        raise ValueError(\"Forward reads file not found on raw data %s\"\n+                         % raw_data.id)\n+\n+    if filetype == \"per_sample_FASTQ\":\n+        if barcode_fps:\n+            raise ValueError(\"per_sample_FASTQ can not have barcodes:\"\n+                             % (', '.join(barcode_fps)))\n+\n+        sn_by_rp = _get_sample_names_by_run_prefix(prep_template)\n+        samples = []\n+        for f in forward_seqs:","path":"qiita_ware/processing_pipeline.py","position":131,"original_position":131,"commit_id":"7747289004911dfdd858754707c11d66e1cc121c","original_commit_id":"7747289004911dfdd858754707c11d66e1cc121c","user":{"login":"ElDeveloper","id":375307,"avatar_url":"https://avatars.githubusercontent.com/u/375307?v=3","gravatar_id":"","url":"https://api.github.com/users/ElDeveloper","html_url":"https://github.com/ElDeveloper","followers_url":"https://api.github.com/users/ElDeveloper/followers","following_url":"https://api.github.com/users/ElDeveloper/following{/other_user}","gists_url":"https://api.github.com/users/ElDeveloper/gists{/gist_id}","starred_url":"https://api.github.com/users/ElDeveloper/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ElDeveloper/subscriptions","organizations_url":"https://api.github.com/users/ElDeveloper/orgs","repos_url":"https://api.github.com/users/ElDeveloper/repos","events_url":"https://api.github.com/users/ElDeveloper/events{/privacy}","received_events_url":"https://api.github.com/users/ElDeveloper/received_events","type":"User","site_admin":false},"body":"After talking with @antgonza offline, it seems like this is OK as is because of the way split_librarie_fastq.py works.","created_at":"2015-06-17T23:07:21Z","updated_at":"2015-06-17T23:07:21Z","html_url":"https://github.com/biocore/qiita/pull/1258#discussion_r32685245","pull_request_url":"https://api.github.com/repos/biocore/qiita/pulls/1258","_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments/32685245"},"html":{"href":"https://github.com/biocore/qiita/pull/1258#discussion_r32685245"},"pull_request":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1258"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1258","id":37581077,"html_url":"https://github.com/biocore/qiita/pull/1258","diff_url":"https://github.com/biocore/qiita/pull/1258.diff","patch_url":"https://github.com/biocore/qiita/pull/1258.patch","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1258","number":1258,"state":"open","locked":false,"title":"issue 1230","user":{"login":"antgonza","id":2014559,"avatar_url":"https://avatars.githubusercontent.com/u/2014559?v=3","gravatar_id":"","url":"https://api.github.com/users/antgonza","html_url":"https://github.com/antgonza","followers_url":"https://api.github.com/users/antgonza/followers","following_url":"https://api.github.com/users/antgonza/following{/other_user}","gists_url":"https://api.github.com/users/antgonza/gists{/gist_id}","starred_url":"https://api.github.com/users/antgonza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antgonza/subscriptions","organizations_url":"https://api.github.com/users/antgonza/orgs","repos_url":"https://api.github.com/users/antgonza/repos","events_url":"https://api.github.com/users/antgonza/events{/privacy}","received_events_url":"https://api.github.com/users/antgonza/received_events","type":"User","site_admin":false},"body":"<del>This is the initial commit but it is still a WIP. However, it will be nice if people can take a look to make sure they agree with these changes. At this point you can upload, link and process (unsuccessfully) already demultiplexed samples without primers. Next steps are: (1) successfully process these kind of samples, and (2) allow to remove 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