From 42e56640f732b40c28bbc23f6ffad748cd7410e9 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: Tue, 28 Jul 2015 10:22:53 +0200 Subject: [PATCH] updating options for Mapping --- docs/pipelines/mapping.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/pipelines/mapping.md b/docs/pipelines/mapping.md index b383dab41..0e20aeecc 100644 --- a/docs/pipelines/mapping.md +++ b/docs/pipelines/mapping.md @@ -41,16 +41,17 @@ All other values should be provided in the config. Specific config values toward | 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`] | | 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) | -| reference_fasta | Path (**required**) | Path to indexed fasta file to be used as reference | | platform | String (optional) | Read group Platform (defaults to `illumina`)| -| platform_unit | String (**required**) | Read group platform unit | -| readgroup_sequencing_center | String (**required**) | Read group sequencing center | -| readgroup_description | String (**required**) | Read group description | -| predicted_insertsize | Integer (**required**) | Read group predicted insert size | +| platform_unit | String (optional) | Read group platform unit | +| readgroup_sequencing_center | String (optional) | Read group sequencing center | +| readgroup_description | String (optional) | Read group description | +| 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. E.g. `-cv reference=<path/to/reference>` would set value `reference`. -- GitLab