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biopet.biopet
Commits
42e56640
Commit
42e56640
authored
Jul 28, 2015
by
Peter van 't Hof
Browse files
updating options for Mapping
parent
67d911cd
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1
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docs/pipelines/mapping.md
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42e56640
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@@ -41,16 +41,17 @@ All other values should be provided in the config. Specific config values toward
| Name | Type | Function |
| ---- | ---- | -------- |
| output_dir | Path (
**required**
) | directory for output files |
| reference_fasta | Path (
**required**
) | Path to indexed fasta file to be used as reference |
| aligner | String (optional) | Which aligner to use. Defaults to
`bwa`
. Choose from [
`bwa`
,
`bwa-aln`
,
`bowtie`
,
`gsnap`
,
`tophat`
,
`stampy`
,
`star`
,
`star-2pass`
] |
| skip_flexiprep | Boolean (optional) | Whether to skip the flexiprep QC step (default = False) |
| skip_markduplicates | Boolean (optional) | Whether to skip the Picard Markduplicates step (default = False) |
| skip_metrics | Boolean (optional) | Whether to skip the metrics gathering step (default = False) |
| reference_fasta | Path (
**required**
) | Path to indexed fasta file to be used as reference |
| platform | String (optional) | Read group Platform (defaults to
`illumina`
)|
| platform_unit | String (
**required**
) | Read group platform unit |
| readgroup_sequencing_center | String (
**required**
) | Read group sequencing center |
| readgroup_description | String (
**required**
) | Read group description |
| predicted_insertsize | Integer (
**required**
) | Read group predicted insert size |
| platform_unit | String (
optional
) | Read group platform unit |
| readgroup_sequencing_center | String (
optional
) | Read group sequencing center |
| readgroup_description | String (
optional
) | Read group description |
| predicted_insertsize | Integer (
optional
) | Read group predicted insert size |
It is possible to provide any config value as a command line argument as well, using the
`-cv`
flag.
E.g.
`-cv reference=<path/to/reference>`
would set value
`reference`
.
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