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biopet.biopet
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8b8d03ae
Commit
8b8d03ae
authored
Apr 03, 2017
by
Giannis Moustakas
Committed by
GitHub
Apr 03, 2017
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Update mapping.md
Fix the list of aligners names to match the mapping.scala class code
parent
50c3adcc
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docs/pipelines/mapping.md
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8b8d03ae
...
...
@@ -49,7 +49,7 @@ All other values should be provided in the config. Specific config values toward
| ---- | ---- | -------- |
| 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`
,
`hisat2`
] |
| aligner | String (optional) | Which aligner to use. Defaults to
`bwa`
. Choose from [
`bwa
-mem`
,
`bwa-aln`
,
`bowtie`
,
`bowtie2
`
,
`gsnap`
,
`tophat`
,
`stampy`
,
`star`
,
`star-2pass`
,
`hisat2`
] |
| 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) |
...
...
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