NextflowUtil

java.lang.Object
- biolockj.util.NextflowUtil

```
public class NextflowUtil
extends Object
```
This utility builds the Nextflow main.nf used in AWS pipelines.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AWS_CONFIG_DIR` Name of the AWS S3 sub-directory used to save pipeline reports
`static String`	`AWS_COPY_INPUTS_TO_S3` `Config` Boolean property: If enabled save all input files to S3: "aws.copyInputsToS3"
`static String`	`AWS_COPY_PIPELINE_TO_S3` `Config` Boolean property: If enabled save pipeline to S3: "aws.copyPipelineToS3"
`static String`	`AWS_COPY_REPORTS_TO_S3` `Config` Boolean property: If enabled save reports to S3: "aws.copyPipelineToS3"
`static String`	`AWS_DB_DIR` Name of the AWS S3 sub-directory used to save pipeline reports
`static String`	`AWS_PIPELINE_DIR` Name of the AWS S3 sub-directory used to save pipeline reports
`static String`	`AWS_PURGE_EFS_INPUTS` `Config` Boolean property: If enabled delete all EFS dirs (except pipelines): "aws.purgeEfsInputs"
`static String`	`AWS_PURGE_EFS_OUTPUT` `Config` Boolean property: If enabled delete all EFS/pipelines: "aws.purgeEfsOutput"
`static String`	`AWS_RAM` `Config` String property: AWS memory set in Nextflow main.nf: "aws.ram"
`static String`	`AWS_REPORT_DIR` Name of the AWS S3 subdirectory used to save pipeline reports
`static String`	`AWS_S3` `Config` String property: AWS S3 pipeline output directory used by Nextflow main.nf: "aws.s3"
`protected static String`	`NF_LOG` The Docker container will generate a nextflow.log file in the root directory, this is the file name

Constructor Summary

Constructors
Constructor and Description

NextflowUtil()

Constructors
Constructor and Description
`NextflowUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`awsSyncS3(String efsPath, boolean waitUntilComplete)` Sync file or directory with S3 bucket. Dir example: aws s3 sync $EFS/config s3://blj-2019-04-05/config File example: aws s3 cp $EFS_META/testMetadata.tsv s3://blj-2019-04-05/metadata/testMetadata.tsv
`static File`	`getMainNf()` Get the Nextflow main.nf file path.
`protected static List<String>`	`getNextflowLines(File template)` Build the main.nf lines from the template file by replacing several parameters.
`static boolean`	`nextflowLogExists()` Return true if the Nextflow log has been saved to the pipeline root directory
`static void`	`purgeEfsData()` Save EFS data to S3 based on pipeline Config.
`static void`	`saveEfsDataToS3()` Save EFS data to S3 based on pipeline Config.
`static void`	`saveNextflowLog()` Save a copy of the Nextflow log file to the Pipeline root directory
`static void`	`startNextflow(List<BioModule> modules)` Call this method to build the Nextflow main.nf for the current pipeline.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - AWS_CONFIG_DIR
```
public static final String AWS_CONFIG_DIR
```
    Name of the AWS S3 sub-directory used to save pipeline reports
    
    See Also:
    
    Constant Field Values
  - AWS_COPY_INPUTS_TO_S3
```
public static final String AWS_COPY_INPUTS_TO_S3
```
    Config Boolean property: If enabled save all input files to S3: "aws.copyInputsToS3"
    
    See Also:
    
    Constant Field Values
  - AWS_COPY_PIPELINE_TO_S3
```
public static final String AWS_COPY_PIPELINE_TO_S3
```
    Config Boolean property: If enabled save pipeline to S3: "aws.copyPipelineToS3"
    
    See Also:
    
    Constant Field Values
  - AWS_COPY_REPORTS_TO_S3
```
public static final String AWS_COPY_REPORTS_TO_S3
```
    Config Boolean property: If enabled save reports to S3: "aws.copyPipelineToS3"
    
    See Also:
    
    Constant Field Values
  - AWS_DB_DIR
```
public static final String AWS_DB_DIR
```
    Name of the AWS S3 sub-directory used to save pipeline reports
    
    See Also:
    
    Constant Field Values
  - AWS_PIPELINE_DIR
```
public static final String AWS_PIPELINE_DIR
```
    Name of the AWS S3 sub-directory used to save pipeline reports
    
    See Also:
    
    Constant Field Values
  - AWS_PURGE_EFS_INPUTS
```
public static final String AWS_PURGE_EFS_INPUTS
```
    Config Boolean property: If enabled delete all EFS dirs (except pipelines): "aws.purgeEfsInputs"
    
    See Also:
    
    Constant Field Values
  - AWS_PURGE_EFS_OUTPUT
```
public static final String AWS_PURGE_EFS_OUTPUT
```
    Config Boolean property: If enabled delete all EFS/pipelines: "aws.purgeEfsOutput"
    
    See Also:
    
    Constant Field Values
  - AWS_RAM
```
public static final String AWS_RAM
```
    Config String property: AWS memory set in Nextflow main.nf: "aws.ram"
    
    See Also:
    
    Constant Field Values
  - AWS_REPORT_DIR
```
public static final String AWS_REPORT_DIR
```
    Name of the AWS S3 subdirectory used to save pipeline reports
    
    See Also:
    
    Constant Field Values
  - AWS_S3
```
public static final String AWS_S3
```
    Config String property: AWS S3 pipeline output directory used by Nextflow main.nf: "aws.s3"
    
    See Also:
    
    Constant Field Values
  - NF_LOG
```
protected static final String NF_LOG
```
    The Docker container will generate a nextflow.log file in the root directory, this is the file name
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - NextflowUtil
```
public NextflowUtil()
```
- Method Detail
  - awsSyncS3
```
public static void awsSyncS3(String efsPath,
                             boolean waitUntilComplete)
                      throws Exception
```
    Sync file or directory with S3 bucket.
    Dir example: aws s3 sync $EFS/config s3://blj-2019-04-05/config
    File example: aws s3 cp $EFS_META/testMetadata.tsv s3://blj-2019-04-05/metadata/testMetadata.tsv
    
    Parameters:
    
    efsPath - File or directory to sync
    
    waitUntilComplete - Boolean if enabled will block until process completes before moving on
    
    Throws:
    
    Exception - if errors occur
  - getMainNf
```
public static File getMainNf()
```
    Get the Nextflow main.nf file path.
    
    Returns:
    
    Nextflow main.nf
  - nextflowLogExists
```
public static boolean nextflowLogExists()
```
    Return true if the Nextflow log has been saved to the pipeline root directory
    
    Returns:
    
    TRUE if log exists in pipeline root directory
  - purgeEfsData
```
public static void purgeEfsData()
                         throws Exception
```
    Save EFS data to S3 based on pipeline Config.
    
    Throws:
    
    Exception - if errors occur
  - saveEfsDataToS3
```
public static void saveEfsDataToS3()
                            throws Exception
```
    Save EFS data to S3 based on pipeline Config.
    
    Throws:
    
    Exception - if errors occur
  - saveNextflowLog
```
public static void saveNextflowLog()
```
    Save a copy of the Nextflow log file to the Pipeline root directory
  - startNextflow
```
public static void startNextflow(List<BioModule> modules)
                          throws Exception
```
    Call this method to build the Nextflow main.nf for the current pipeline.
    
    Parameters:
    
    modules - Pipeline modules
    
    Throws:
    
    Exception - if errors occur
  - getNextflowLines
```
protected static List<String> getNextflowLines(File template)
                                        throws Exception
```
    Build the main.nf lines from the template file by replacing several parameters.
    
    Parameters:
    
    template - Generated .main.nf template
    
    Returns:
    
    List of lines to save in final main.nf
    
    Throws:
    
    Exception - if errors occur

Class NextflowUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

AWS_CONFIG_DIR

AWS_COPY_INPUTS_TO_S3

AWS_COPY_PIPELINE_TO_S3

AWS_COPY_REPORTS_TO_S3

AWS_DB_DIR

AWS_PIPELINE_DIR

AWS_PURGE_EFS_INPUTS

AWS_PURGE_EFS_OUTPUT

AWS_RAM

AWS_REPORT_DIR

AWS_S3

NF_LOG

Constructor Detail

NextflowUtil

Method Detail

awsSyncS3

getMainNf

nextflowLogExists

purgeEfsData

saveEfsDataToS3

saveNextflowLog

startNextflow

getNextflowLines