Class that holds information about a the output of a nf-core pipeline
| Modifiers | Name | Description |
|---|---|---|
private static java.lang.String |
FQDN_FILES |
|
private static java.lang.String |
FQDN_FOLDERS |
|
private static java.util.Set |
nfCoreFileTypes |
|
private static java.util.Set |
nfCoreFolderTypes |
|
private PipelineInformationFolder |
pipelineInformationFolder |
|
private java.util.List<DataFolder> |
processFolders |
|
private QualityControlFolder |
qualityControlFolder |
|
private RunId |
runId |
|
private SampleIds |
sampleIds |
| Constructor and description |
|---|
NfCorePipelineResult
(PipelineInformationFolder pipelineInformationFolder, QualityControlFolder qualityControlFolder, java.util.List<DataFolder> processFolders, RunId runId, SampleIds sampleIds) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
static NfCorePipelineResult |
createFrom(java.util.Map bioinformaticPipelineOutput)Static factory method that creates a new nfcoreExperiment instance from the bioinformatic pipeline output. |
|
PipelineInformationFolder |
getPipelineInformation()Provides access to the information stored in the pipeline information folder |
|
java.util.List<DataFolder> |
getProcessFolders()Provides access to the information stored in the process folders |
|
QualityControlFolder |
getQualityControlFolder()Provides access to the information stored in the quality Control folder |
|
RunId |
getRunId()Provides access to the information stored in the runId file |
|
SampleIds |
getSampleIds()Provides access to the information stored in the sampleIds file |
|
private static java.util.List |
parseChildren(java.util.List<java.util.Map> children) |
|
private static DataFile |
parseFile(java.util.Map fileTree) |
|
private static DataFolder |
parseFolder(java.util.Map fileTree) |
|
private static java.util.Optional<DataFolder> |
tryToCreateDataFolder(java.lang.reflect.Method method, java.lang.String name, java.lang.String relativePath, java.util.List children) |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Static factory method that creates a new nfcoreExperiment instance from the bioinformatic pipeline output. See this @{link example} for a JSON representation of a valid map structure
Map - bioinformaticPipelineOutputProvides access to the information stored in the pipeline information folder
Provides access to the information stored in the process folders
Provides access to the information stored in the quality Control folder
Provides access to the information stored in the runId file
Provides access to the information stored in the sampleIds file