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biopet.biopet
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28f14362
Commit
28f14362
authored
Nov 12, 2015
by
Peter van 't Hof
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docs/general/config.md
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@@ -85,9 +85,10 @@ Global setting examples are:
#### References
Pipelines and tools that use references should now use the reference module.
This gives a more fine-grained control over references and enables a user to curate the references in a structural way.
E.g. pipelines and tools which use
s
FASTA references should now set value
`"reference_fasta"`
.
E.g. pipelines and tools which use
a
FASTA references should now set value
`"reference_fasta"`
.
Additionally, we can set
`"reference_name"`
for the name to be used (e.g.
`"hg19"`
). If unset, Biopet will default to
`unknown`
.
It is also possible to set the
`"species"`
flag. Again, we will default to
`unknown`
if unset.
#### Example settings config
```
json
{
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