diff --git a/modules/controlfreec/meta.yml b/modules/controlfreec/meta.yml index 4d1e8674..3e218037 100644 --- a/modules/controlfreec/meta.yml +++ b/modules/controlfreec/meta.yml @@ -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. - 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": , - "breakpointthreshold": , - "breakpointtype": , - "coefficientofvariation": , - "contamination": , - "contaminationadjustment": , - "degree": , - "forcegccontentnormalization": , - "gccontentprofile": , - "intercept": , - "mincnalength": , - "minmappabilityperwindow": , - "minexpectedgc": , - "maxexpectedgc": , - "minimalsubclonepresence": , - "noisydata": , - "ploidy": , - "printNA": , - "readcountthreshold": , - "sex": , - "step": , - "telocentromeric": , - "uniquematch": , - "window": - ], - "control":[ - "inputformat": , - "mateorientation": , - ], - "sample":[ - "inputformat": , - "mateorientation": , - ], - "BAF":[ - "minimalcoverageperposition": , - "minimalqualityperposition": , - "shiftinquality": + ``` + { + [ + "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