biolockj#
| Property | Description |
|---|---|
| biolockj.version | string Property giving the biolockj version that was used to generate the config file. default: null |
cluster#
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.host | string The remote cluster host URL (used for ssh, scp, rsync, etc) default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.returnsBatchIds | boolean Options Y/N. Does the cluster.batchCommand return a job id. If Y, if a job is submitted and no id is returned, that will be treated as a failure and the pipeline will stop. default: Y |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
demultiplexer#
| Property | Description |
|---|---|
| demultiplexer.barcodeCutoff | numeric Options: (0.0 - 1.0); if defined, pipeline will fail if the percentage of reads with a barcode is less than this cutoff. default: 0.05 |
| demultiplexer.barcodeRevComp | boolean Options: Y/N. Use reverse compliment of metadata.barcodeColumn if demultimplexer.strategy = barcode_in_header or barcode_in_seq. default: null |
| demultiplexer.strategy | string Options: barcode_in_header, barcode_in_seq, id_in_header, do_not_demux.If using barcodes, they must be provided in the metadata file within column defined by metadata.barcodeColumn. default: null |
docker#
| Property | Description |
|---|---|
| docker.imageName | string The name of a docker image to override whatever a module says to use. Only use the module-specific-override form of this property. default: null |
| docker.imageOwner | string Name of the Docker Hub user that owns the docker containers. Only use the module-specific-override form of this property. default: null |
| docker.imageTag | string Image tag, a specific version of Docker images. Only use the module-specific-override form of this property. default: null |
| docker.mountSock | boolean should /var/run/docker.sock be mounted for modules. default: N |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
exe#
| Property | Description |
|---|---|
| exe.Rscript | executable Path for the "Rscript" executable; if not supplied, any script that needs the Rscript command will assume it is on the PATH. default: null |
| exe.awk | executable Path for the "awk" executable; if not supplied, any script that needs the awk command will assume it is on the PATH. default: null |
| exe.docker | executable Path for the "docker" executable; if not supplied, any script that needs the docker command will assume it is on the PATH. default: null |
| exe.gzip | executable Path for the "gzip" executable; if not supplied, any script that needs the gzip command will assume it is on the PATH. default: null |
| exe.java | executable Path for the "java" executable; if not supplied, any script that needs the java command will assume it is on the PATH. default: null |
| exe.python | executable Path for the "python" executable; if not supplied, any script that needs the python command will assume it is on the PATH. default: null |
humann2#
| Property | Description |
|---|---|
| humann2.disableGeneFamilies | boolean disable HumanN2 Gene Family report default: null |
| humann2.disablePathAbundance | boolean disable HumanN2 Pathway Abundance report default: null |
| humann2.disablePathCoverage | boolean disable HumanN2 Pathway Coverage report default: null |
input#
| Property | Description |
|---|---|
| input.allowDuplicateNames | boolean Should files with the same name be permitted in inputs. File names are used to link data to metadata, and duplicated names create ambiguity. However in some pipelines, duplicates are appropriate. default: N |
| input.dirPaths | list of file paths List of one or more directories containing the pipeline input data. default: null |
| input.ignoreFiles | list file names to ignore if found in input directories default: null |
| input.requireCompletePairs | boolean Require all sequence input files have matching paired reads default: Y |
| input.suffixFw | regex file suffix used to identify forward reads ininput.dirPaths default: _R1 |
| input.suffixRv | regex file suffix used to identify reverse reads ininput.dirPaths default: _R2 |
| input.trimPrefix | string Prefix to trim from sequence file names or headers to obtain Sample ID; this string can appear anywhere in the filename and all text before it will be removed. default: null |
| input.trimSuffix | string Suffix to trim from sequence file names or headers to obtain Sample ID; this string can appear anywhere in the filename and all text after it will be removed. default: null |
metadata#
| Property | Description |
|---|---|
| metadata.barcodeColumn | string metadata column with identifying barcodes default: BarcodeSequence |
| metadata.columnDelim | string defines how metadata columns are separated; Typically files are tab or comma separated. default: \t |
| metadata.commentChar | string metadata file comment indicator; Empty string is a valid option indicating no comments in metadata file. default: null |
| metadata.fileNameColumn | list name of the metadata column(s) with input file names default: null |
| metadata.filePath | file path If absolute file path, use file as metadata. If directory path, must find exactly 1 file within, to use as metadata. default: null |
| metadata.nullValue | string metadata cells with this value will be treated as empty default: NA |
| metadata.required | boolean If Y, require metadata row for each sample with sequence data in input dirs; If N, samples without metadata are ignored. default: N |
| metadata.useEveryRow | boolean If Y, require a sequence file for every SampleID (every row) in metadata file; If N, metadata can include extraneous SampleIDs. default: null |
pipeline#
| Property | Description |
|---|---|
| pipeline.copyInput | boolean copy input files into pipeline root directory default: null |
| pipeline.defaultDemultiplexer | string Java class name for default module used to demultiplex data default: biolockj.module.implicit.Demultiplexer |
| pipeline.defaultFastaConverter | string Java class name for default module used to convert files into fasta format default: biolockj.module.seq.AwkFastaConverter |
| pipeline.defaultProps | list of file paths file path of default property file(s); Nested default properties are supported (so the default property file can also have a default, and so on). default: null |
| pipeline.defaultSeqMerger | string Java class name for default module used combined paired read files default: biolockj.module.seq.PearMergeReads |
| pipeline.defaultStatsModule | string Java class name for default module used generate p-value and other stats default: biolockj.module.report.r.R_CalculateStats |
| pipeline.deleteTempFiles | boolean delete files in temp directories default: null |
| pipeline.detachJavaModules | boolean If true Java modules do not run with main BioLockJ Java application. Instead they run on compute nodes on the CLUSTER or AWS environments. default: Y |
| pipeline.disableAddImplicitModules | boolean If set to true, implicit modules will not be added to the pipeline. default: null |
| pipeline.disableAddPreReqModules | boolean If set to true, prerequisite modules will not be added to the pipeline. default: null |
| pipeline.downloadDir | file path local directory used as the destination in the download command default: $HOME/projects/downloads |
| pipeline.env | string Environment in which a pipeline is run. Options: cluster, aws, local default: local |
| pipeline.envVars | list list of variables that should be passed into the runtime environment for all modules. default: BLJ |
| pipeline.inputTypes | list List of file types. This manually overrides the recommended auto-detection. default: null |
| pipeline.limitDebugClasses | list limit classes that log debug statements default: null |
| pipeline.logLevel | string Options: DEBUG, INFO, WARN, ERROR default: INFO |
| pipeline.permissions | string Set chmod -R command security bits on pipeline root directory (Ex. 770) default: 770 |
| pipeline.setSeed | integer set the seed for a random process. Must be positive integer. default: null |
| pipeline.useEnvVars | boolean when evaluating variables in the ${VAR} format, should environment variables be used. Regardless, priority is given to variable values defined in the config file. default: Y |
| pipeline.userProfile | file path Bash profile - may be ~/.bash_profile or ~/.bashrc or others default: null |
qiime#
| Property | Description |
|---|---|
| qiime.alphaMetrics | list alpha diversity metrics to calculate through qiime; For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html default: shannon |
| qiime.plotAlphaMetrics | boolean default: Y |
r#
| Property | Description |
|---|---|
| r.colorBase | string base color used for labels & headings in the PDF report; Must be a valid color in R. default: black |
| r.colorFile | file path path to a tab-delimited file giving the color to use for each value of each metadata field plotted. default: null |
| r.colorHighlight | string color is used to highlight significant OTUs in plot default: red |
| r.colorPalette | string palette argument passed to get_palette {ggpubr} to select colors for some output visualiztions default: null |
| r.colorPoint | string default color of scatterplot and strip-chart plot points default: black |
| r.debug | boolean Options: Y/N. If Y, will generate R Script log files default: Y |
| r.excludeFields | list Fields from the metadata that will be excluded from any auto-determined typing, or plotting; R reports must contain at least one valid nominal or numeric metadata field. default: null |
| r.nominalFields | list Override default property type by explicitly listing it as nominal. default: null |
| r.numericFields | list Override default property type by explicitly listing it as numeric. default: null |
| r.pch | integer Sets R plot pch parameter for PDF report default: 21 |
| r.pvalCutoff | numeric p-value cutoff used to assign label r.colorHighlight default: 0.05 |
| r.rareOtuThreshold | numeric If >=1, R will filter OTUs found in fewer than this many samples. If <1, R will interperate the value as a percentage and discard OTUs not found in at least that percentage of samples default: 1 |
| r.reportFields | list Metadata fields to include in reports; Fields listed here must exist in the metadata file. R reports must contain at least one valid field. default: null |
| r.saveRData | boolean If Y, all R script generating BioModules will save R Session data to the module output directory to a file using the extension ".RData" default: null |
| r.timeout | integer defines the number of minutes before R script fails due to timeout. If set to 0, an estimate is used. default: 0 |
| r.useUniqueColors | boolean force to use a unique color for every value in every field plotted; only recommended for low numbers of metadata columns/values. default: null |
r_PlotMds#
| Property | Description |
|---|---|
| r_PlotMds.reportFields | list Metadata column names indicating fields to include in the MDS report; Fields listed here must exist in the metadata file. default: null |
report#
| Property | Description |
|---|---|
| report.logBase | string Options: 10,e,null. If e, use natural log (base e); if 10, use log base 10; if not set, counts will not be converted to a log scale. default: 10 |
| report.minCount | integer minimum table count allowed, if a count less that this value is found, it is set to 0. default: 2 |
| report.numHits | boolean Options: Y/N. If Y, and add Num_Hits to metadata default: Y |
| report.numReads | boolean Options: Y/N. If Y, and add Num_Reads to metadata default: Y |
| report.scarceCountCutoff | numeric Minimum percentage of samples that must contain a count value for it to be kept. default: 0.25 |
| report.scarceSampleCutoff | numeric Minimum percentage of data columns that must be non-zero to keep the sample. default: 0.25 |
| report.taxonomyLevels | list Options: domain,phylum,class,order,family,genus,species. Generate reports for listed taxonomy levels default: phylum,class,order,family,genus |
| report.unclassifiedTaxa | boolean report unclassified taxa default: Y |
script#
| Property | Description |
|---|---|
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.fileRefreshDelay | integer delay this many seconds after scripts complete to allow the file system to reflect changes from a worker node/container/virtual machine. default: 1 |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
validation#
| Property | Description |
|---|---|
| validation.compareOn | list Which columns in the expectation file should be used for the comparison. Options: name, size, md5. Default: use all columns in the expectation file. default: null |
| validation.disableValidation | boolean Turn off validation. No validation file output is produced. Options: Y/N. default: N default: null |
| validation.expectationFile | file path file path that gives the expected values for file metrics (probably generated by a previous run of the same pipeline) default: null |
| validation.reportOn | list Which attributes of the file should be included in the validation report file. Options: name, size, md5 default: null |
| validation.sizeWithinPercent | numeric What percentage difference is permitted between an output file and its expectation. Options: any positive number default: null |
| validation.stopPipeline | boolean If enabled, the validation utlility will stop the pipeline if any module fails validation. Options: Y/N default: N |
aws#
| Property | Description |
|---|---|
| aws.copyDbToS3 | boolean If true, save all input files to S3 default: null |
| aws.copyPipelineToS3 | boolean If enabled save pipeline to S3 default: null |
| aws.copyReportsToS3 | boolean If enabled save reports to S3 default: null |
| aws.ec2AcquisitionStrategy | string The AWS acquisition strategy (SPOT or DEMAND) sets the service SLA for procuring new EC2 instances default: null |
| aws.ec2InstanceID | string ID of an existing ec2 instance to use as the head node default: null |
| aws.ec2InstanceType | string AWS instance type determines initial resource class (t2.micro is common) default: null |
| aws.ec2SpotPer | __ default: null |
| aws.ec2TerminateHead | boolean default: null |
| aws.profile | file path default: null |
| aws.purgeEfsInputs | boolean If enabled delete all EFS dirs (except pipelines) default: null |
| aws.purgeEfsOutput | boolean If enabled delete all EFS/pipelines default: null |
| aws.ram | string AWS memory set in Nextflow main.nf default: null |
| aws.region | string default: null |
| aws.s3 | string AWS S3 pipeline output directory used by Nextflow main.nf default: null |
| aws.s3TransferTimeout | integer Set the max number of minutes to allow for S3 transfers to complete. default: null |
| aws.saveCloud | boolean default: null |
| aws.stack | string An existing aws cloud stack ID default: null |
| aws.walltime | __ default: null |