docs/source/api.rst

   1 Runfolder Processing
   2 ====================
   3
   4 Runfolder
   5 ---------
   6
   7 The PipelineRun class is designed to combine information
   8 from the following importers.
   9
  10 * Image Analysis (one of the following)
  11
  12   * :class:`Firecrest`
  13   * :class:`IPAR`
  14
  15 * BaseCaller
  16
  17   * :class:`Bustard`
  18
  19 * Sequence Alignment
  20
  21   * :class:`Gerald`
  22
  23 .. automodule:: htsworkflow.pipelines.runfolder
  24    :members:
  25
  26 .. _Firecrest:
  27
  28 Firecrest
  29 ---------
  30
  31 .. automodule:: htsworkflow.pipelines.firecrest
  32    :members:
  33
  34 .. _IPAR:
  35
  36 IPAR
  37 ----
  38
  39 .. automodule:: htsworkflow.pipelines.ipar
  40    :members:
  41
  42 .. _Bustard:
  43
  44 Bustard
  45 -------
  46 .. automodule:: htsworkflow.pipelines.bustard
  47    :members:
  48
  49 .. _Gerald:
  50
  51 Gerald
  52 ------
  53
  54 .. automodule:: htsworkflow.pipelines.gerald
  55    :members:
  56
  57 .. _Eland:
  58
  59 Eland
  60 -----
  61
  62 .. automodule:: htsworkflow.pipelines.eland
  63    :members:
  64
  65 .. _Summary:
  66
  67 Summary
  68 -------
  69
  70 .. automodule:: htsworkflow.pipelines.summary
  71    :members:
  72
  73 Sequence Archival
  74 =================
  75
  76 srf
  77 ---
  78
  79 .. automodule:: htsworkflow.pipelines.srf
  80    :members:
  81
  82 Fastq conversion
  83 ================
  84
  85 srf2fastq
  86 ---------
  87
  88 .. automodule:: htsworkflow.pipelines.srf2fastq
  89    :members:
  90
  91 qseq2fastq
  92 ----------
  93
  94 .. automodule:: htsworkflow.pipelines.qseq2fastq
  95    :members:
  96
  97 desplit_fastq
  98 -------------
  99
 100 .. automodule:: htsworkflow.pipelines.desplit_fastq
 101    :members:
 102
 103 sequences
 104 ---------
 105
 106 .. automodule:: htsworkflow.pipelines.sequences
 107    :members:
 108
 109 Utilities
 110 =========
 111
 112 .. automodule:: htsworkflow.pipelines.genome_mapper
 113    :members:
 114
 115 .. automodule:: htsworkflow.pipelines.genomemap
 116    :members:
 117
 118 .. automodule:: htsworkflow.pipelines.samplekey
 119    :members:
 120
 121 .. automodule:: htsworkflow.pipelines.recipe_parser
 122    :members:
 123
 124 Run Automation
 125 ==============
 126
 127 .. automodule:: htsworkflow.pipelines.configure_run
 128    :members:
 129
 130 .. automodule:: htsworkflow.pipelines.retrieve_config
 131    :members:
 132
 133 .. automodule:: htsworkflow.pipelines.run_status
 134    :members: