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Last active March 2, 2017 17:04
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bcbio.md

bcbio for Dummies

(like me)

download template. This creates a directory (in the example below, the directory is my_dummy_dir), in which you will find a .yaml file.

bcbio_nextgen.py -w template illumina-rnaseq my_dummy_dir

(where is this documented?)

Edit the .yaml file (with a script, possibly). For example, you might want to replace tophat2 with star (which is what WW does).

The template .yaml is then converted to a full config with:

bcbio_nextgen.py -w template my_dummy_dir/config/my_dummy_dir-template.yaml ../bcbio_human_test/fastq/sampleInfo.csv list_of_files ...

which creates, based on the name of the CSV file, sampleInfo/config/sampleInfo.yaml file.

run bcbio_nextgen.py ../config/sampleInfo.yaml

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