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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: input:
- args: - args:
type: map type: map
description: | description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. 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: 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. For default values, please check the documentation above.
``` ```
{ {
[ [
"general" :[ "general" :[
"bedgraphoutput": <optional>, "bedgraphoutput": (optional),
"breakpointthreshold": <optional>, "breakpointthreshold": (optional),
"breakpointtype": <optional>, "breakpointtype": (optional),
"coefficientofvariation": <optional>, "coefficientofvariation": (optional),
"contamination": <optional>, "contamination": (optional),
"contaminationadjustment": <optional>, "contaminationadjustment": (optional),
"degree": <optional>, "degree": (optional),
"forcegccontentnormalization": <optional>, "forcegccontentnormalization": (optional),
"gccontentprofile": <optional>, "gccontentprofile": (optional),
"intercept": <optional>, "intercept": (optional),
"mincnalength": <optional>, "mincnalength": (optional),
"minmappabilityperwindow": <optional>, "minmappabilityperwindow": (optional),
"minexpectedgc": <optional>, "minexpectedgc": (optional),
"maxexpectedgc": <optional>, "maxexpectedgc": (optional),
"minimalsubclonepresence": <optional>, "minimalsubclonepresence": (optional),
"noisydata": <optional>, "noisydata": (optional),
"ploidy": <optional>, "ploidy": (optional),
"printNA": <optional>, "printNA": (optional),
"readcountthreshold": <optional >, "readcountthreshold": (optional),
"sex": <optional>, "sex": (optional),
"step": <optional value>, "step": (optional),
"telocentromeric": <optional>, "telocentromeric": (optional),
"uniquematch": <optional>, "uniquematch": (optional),
"window": <optional> "window": (optional)
], ],
"control":[ "control":[
"inputformat": <required>, "inputformat": (required),
"mateorientation": <optional>, "mateorientation": (optional),
], ],
"sample":[ "sample":[
"inputformat": <required>, "inputformat": (required),
"mateorientation": <optional>, "mateorientation": (optional),
], ],
"BAF":[ "BAF":[
"minimalcoverageperposition": <optional>, "minimalcoverageperposition": (optional),
"minimalqualityperposition": <optional>, "minimalqualityperposition": (optional),
"shiftinquality": <optional> "shiftinquality": (optional)
]
] ]
] }
} ```
```
- meta: - meta:
type: map type: map