Commit 0876b768 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge branch 'develop' into fix-BIOPET-628

parents f07f6b2d 7edefbcd
...@@ -49,7 +49,7 @@ All other values should be provided in the config. Specific config values toward ...@@ -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 | | output_dir | Path (**required**) | directory for output files |
| reference_fasta | Path (**required**) | Path to indexed fasta file to be used as reference | | 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_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) |
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