Commit 8b8d03ae authored by Giannis Moustakas's avatar Giannis Moustakas Committed by GitHub
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Update mapping.md

Fix the list of aligners names to match the mapping.scala class code
parent 50c3adcc
......@@ -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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