autohagfish

sphinx/templates/autohagfish.rst

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+autohagfish
+------------------------------------------------
+
+**Automatically run bowtie & hagfish combined**
+
+
+    Run the preparatory steps for hagfish
+
+
+
+Commands
+~~~~~~~~
+
+**clean**
+  remove all Hagfish files
+
+
+**finish**
+  finish up - find gaps - combine plots - create a report
+
+
+**run**
+  Run hagfish
+
+
+
+Filesets
+~~~~~~~~
+
+
+**fasta**
+  fasta sequence of the reference
+
+
+  | *type*: `single`
+  | *category*: `prerequisite`
+  | *optional*: `False`
+  | *pattern*: `{}`
+
+
+
+
+**fw_fq**
+  forward fq input
+
+
+
+
+
+**outbase**
+  basename for output files
+
+
+  | *type*: `map`
+  | *source*: `fw_fq`
+  | *category*: `output`
+  | *optional*: `True`
+  | *pattern*: `./*`
+
+
+
+
+**rev_fq**
+  reverse fq input
+
+
+  | *type*: `map`
+  | *source*: `fw_fq`
+  | *category*: `input`
+  | *optional*: `True`
+  | *pattern*: `*/*2.fq`
+
+
+
+
+
+Parameters
+~~~~~~~~~~
+
+
+
+**max_ok**
+  Maximal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate
+
+  | *type*: `int`
+  | *default*: `0`
+  | *optional*: `True`
+
+
+
+**min_ok**
+  Minimal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate
+
+  | *type*: `int`
+  | *default*: `0`
+  | *optional*: `True`
+
+
+
+**threads**
+  no threads to use
+
+  | *type*: `integer`
+  | *default*: `8`
+  | *optional*: `True`
+
+
+
+miscellaneous
+~~~~~~~~~~~~~
+
+**Backend**
+  ruff
+**Author**
+  Mark Fiers
+**Creation date**
+  Tue Mar 29 16:34:19 2011
+**Modification date**
+  Thu, 19 May 2011 20:49:04 +1200