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fix indent error, avoiding html tag confusion (#1393)

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Matthias Hörtenhuber 2022-03-15 11:56:42 +01:00 committed by GitHub
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98
modules/controlfreec/meta.yml
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@ -17,57 +17,57 @@ tools:
input:
- args:
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
<optional> parameters can be removed from the map, if they are not set. All value must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
For default values, please check the documentation above.
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`:
For default values, please check the documentation above.
```
{
[
"general" :[
"bedgraphoutput": <optional>,
"breakpointthreshold": <optional>,
"breakpointtype": <optional>,
"coefficientofvariation": <optional>,
"contamination": <optional>,
"contaminationadjustment": <optional>,
"degree": <optional>,
"forcegccontentnormalization": <optional>,
"gccontentprofile": <optional>,
"intercept": <optional>,
"mincnalength": <optional>,
"minmappabilityperwindow": <optional>,
"minexpectedgc": <optional>,
"maxexpectedgc": <optional>,
"minimalsubclonepresence": <optional>,
"noisydata": <optional>,
"ploidy": <optional>,
"printNA": <optional>,
"readcountthreshold": <optional >,
"sex": <optional>,
"step": <optional value>,
"telocentromeric": <optional>,
"uniquematch": <optional>,
"window": <optional>
],
"control":[
"inputformat": <required>,
"mateorientation": <optional>,
],
"sample":[
"inputformat": <required>,
"mateorientation": <optional>,
],
"BAF":[
"minimalcoverageperposition": <optional>,
"minimalqualityperposition": <optional>,
"shiftinquality": <optional>
```
{
[
"general" :[
"bedgraphoutput": (optional),
"breakpointthreshold": (optional),
"breakpointtype": (optional),
"coefficientofvariation": (optional),
"contamination": (optional),
"contaminationadjustment": (optional),
"degree": (optional),
"forcegccontentnormalization": (optional),
"gccontentprofile": (optional),
"intercept": (optional),
"mincnalength": (optional),
"minmappabilityperwindow": (optional),
"minexpectedgc": (optional),
"maxexpectedgc": (optional),
"minimalsubclonepresence": (optional),
"noisydata": (optional),
"ploidy": (optional),
"printNA": (optional),
"readcountthreshold": (optional),
"sex": (optional),
"step": (optional),
"telocentromeric": (optional),
"uniquematch": (optional),
"window": (optional)
],
"control":[
"inputformat": (required),
"mateorientation": (optional),
],
"sample":[
"inputformat": (required),
"mateorientation": (optional),
],
"BAF":[
"minimalcoverageperposition": (optional),
"minimalqualityperposition": (optional),
"shiftinquality": (optional)
]
]
]
}
```
}
```
- meta:
type: map