Commit 7edefbcd authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge pull request #54 from biopet/johnmous-patch-1

Update mapping.md
parents 50c3adcc 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) |
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment