bam2wig requirements

docs/pipelines/bam2wig.md

@@ -5,32 +5,42 @@
 Bam2Wig is a small pipeline consisting of three steps that is used to convert BAM files into track coverage files: bigWig, wiggle, and TDF. While this seems like a task that should be tool, at the time of writing, there are no command line tools that can do such conversion in one go. Thus, the Bam2Wig pipeline was written.
 
 ## Configuration
-
 The required configuration file for Bam2Wig is really minimal, only a single JSON file containing an `output_dir` entry:
 
 ~~~
 {"output_dir": "/path/to/output/dir"}
 ~~~
+For technical reasons, single sample pipelines, such as this mapping pipeline do **not** take a sample config.
+Input files are in stead given on the command line as a flag.
+Bam2wig requires a one to set the `--bamfile` command line argument to point to the to-be-converted BAM file.
 
 ## Running Bam2Wig
 
 As with other pipelines, you can run the Bam2Wig pipeline by invoking the `pipeline` subcommand. There is also a general help available which can be invoked using the `-h` flag:
 
-~~~
-$ java -jar /path/to/biopet.jar pipeline sage -h
+~~~bash
+$ java -jar /path/to/biopet.jar pipeline bam2wig -h
+
+Arguments for Bam2Wig:
+ --bamfile <bamfile>                   Input bam file
+ -config,--config_file <config_file>   JSON / YAML config file(s)
+ -cv,--config_value <config_value>     Config values, value should be formatted like 'key=value' or
+                                       'path:path:key=value'
+ -DSC,--disablescatter                 Disable all scatters
+
 ~~~
 
 If you are on SHARK, you can also load the `biopet` module and execute `biopet pipeline` instead:
 
-~~~
+~~~bash
 $ module load biopet/v0.3.0
 $ biopet pipeline bam2wig
 
 ~~~
 
 To run the pipeline:
-~~~
- biopet pipeline bam2wig -config </path/to/config.json> -qsub -jobParaEnv BWA -run
+~~~bash
+ biopet pipeline bam2wig -config </path/to/config.json> --bamfile </path/to/bam.bam> -qsub -jobParaEnv BWA -run
 ~~~
 
 ## Output Files