Commit 42e56640 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

updating options for Mapping

parent 67d911cd
...@@ -41,16 +41,17 @@ All other values should be provided in the config. Specific config values toward ...@@ -41,16 +41,17 @@ All other values should be provided in the config. Specific config values toward
| Name | Type | Function | | 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`] | | 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_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_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) | | 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 | String (optional) | Read group Platform (defaults to `illumina`)|
| platform_unit | String (**required**) | Read group platform unit | | platform_unit | String (optional) | Read group platform unit |
| readgroup_sequencing_center | String (**required**) | Read group sequencing center | | readgroup_sequencing_center | String (optional) | Read group sequencing center |
| readgroup_description | String (**required**) | Read group description | | readgroup_description | String (optional) | Read group description |
| predicted_insertsize | Integer (**required**) | Read group predicted insert size | | 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. 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`. E.g. `-cv reference=<path/to/reference>` would set value `reference`.
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