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biopet.biopet
Commits
8b8d03ae
Commit
8b8d03ae
authored
Apr 03, 2017
by
Giannis Moustakas
Committed by
GitHub
Apr 03, 2017
Browse files
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
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@@ -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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