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Commit ef854547 authored by Sander Bollen's avatar Sander Bollen
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......@@ -43,15 +43,15 @@ All other values should be provided in the config. Specific config values toward
| skipmarkduplicates | Boolean (optional) | Whether to skip the Picard Markduplicates step (default = False) |
| skipmetrics | Boolean (optional) | Whether to skip the metrics gathering step (defualt = False) |
| reference | Path (**required**) | Path to indexed fasta file to be used as reference |
| rgid | String (**required**) | Readgroup ID |
| rglb | String (**required**) | Readgroup Library |
| rgpl | String (**required**) | Readgroup Platform |
| rgpu | String (**required**) | Readgroup platform unit |
| rgsm | String (**required**) | Readgroup sample |
| rgcn | String (**required**) | Readgroup sequencing center |
| rgds | String (**required**) | Readgroup description |
| rgdt | ISO8601 date (**required**) | Readgroup sequencing date |
| rgpi | Integer (**required**) | Readgroup predicted insert size |
| rgid | String (**required**) | Read group ID |
| rglb | String (**required**) | Read group Library |
| rgpl | String (**required**) | Read group Platform |
| rgpu | String (**required**) | Read group platform unit |
| rgsm | String (**required**) | Read group sample |
| rgcn | String (**required**) | Read group sequencing center |
| rgds | String (**required**) | Read group description |
| rgdt | ISO8601 date (**required**) | Read group sequencing date |
| rgpi | Integer (**required**) | Read group predicted insert size |
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`.
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