Inputs

Input YAML

Field	Type	Description
patient_id	string	Patient ID (will be standardized according to data storage structure in the near future)
normal_BAM	path	Set to absolute path to normal BAM
tumor_BAM	path	Set to absolute path to tumour BAM
recalibration_table	path	(Optional) Absolute path to recalibration table

Input without pre-existing recalibration table(s):

---
patient_id: "patient_id"
input:
  BAM:
    normal:
      - "/absolute/path/to/BAM"
      - "/absolute/path/to/BAM"
    tumor:
      - "/absolute/path/to/BAM"
      - "/absolute/path/to/BAM"

Input with existing recalibration table(s):

---
patient_id: "patient_id"
input:
  BAM:
    normal:
      - "/absolute/path/to/BAM"
      - "/absolute/path/to/BAM"
    tumor:
      - "/absolute/path/to/BAM"
      - "/absolute/path/to/BAM"
  recalibration_table:
    - "/absolute/path/to/recalibration/table1"
    - "/absolute/path/to/recalibration/table2"

For normal-only or tumour-only samples, exclude the fields for the other state.

Config

Input Parameter	Required	Type	Description
`dataset_id`	Yes	string	Dataset ID
`blcds_registered_dataset`	Yes	boolean	Set to true when using BLCDS folder structure; use false for now
`output_dir`	Yes	string	Need to set if `blcds_registered_dataset = false`
`save_intermediate_files`	Yes	boolean	Set to false to disable publishing of intermediate files; true otherwise; disabling option will delete intermediate files to allow for processing of large BAMs
`aligner`	Yes	string	Original aligner used to align input BAMs; formatted as \-\
`cache_intermediate_pipeline_steps`	No	boolean	Set to true to enable process caching from Nextflow; defaults to false
`is_emit_original_quals`	Yes	boolean	Set to true to emit original quality scores; false to omit
`is_DOC_run`	Yes	boolean	Set to true to run GATK DepthOfCoverage (very time-consuming for large BAMs); false otherwise
`parallelize_by_chromosome`	Yes	boolean	Whether the parallelize by chromosome or by scattering intervals
`scatter_count`	Yes	integer	Number of intervals to divide into for parallelization
`intervals`	Yes	path	Use all .list in inputs for WGS; Set to absolute path to targeted exome interval file (with .interval_list, .list, .intervals, or .bed suffix)
`gatk_ir_compression`	No	integer	Compression level for BAMs output by IndelRealigner. Default: 0. Range: 0-9
`reference_fasta`	Yes	path	Absolute path to reference genome fasta file, e.g., `/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta`
`bundle_mills_and_1000g_gold_standard_indels_vcf_gz`	Yes	path	Absolute path to Mills & 1000G Gold Standard Indels file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
`bundle_known_indels_vcf_gz`	Yes	path	Absolute path to known indels file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz`
`bundle_v0_dbsnp138_vcf_gz`	Yes	path	Absolute path to dbsnp file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz`
`bundle_contest_hapmap_3p3_vcf_gz`	Yes	path	Absolute path to HapMap 3.3 biallelic sites file, e.g., `/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz`
`work_dir`	optional	path	Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is `/scratch` and should only be changed for testing/development. Changing this directory to `/hot` or `/tmp` can lead to high server latency and potential disk space limitations, respectively.
`base_resource_update`	optional	namespace	Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in `template.config` and below.

The below parameters have default values defined in default.config and generally do not need to be set by the user.

Optional Parameter	Type	Description
`metapipeline_delete_input_bams`	boolean	Set to true to delete the input BAM files once the initial processing step is complete. WARNING: This option should NOT be used for individual runs of recalibate-BAM; it's intended for metapipeline-DNA to optimize disk space usage by removing files that are no longer needed from the `workDir`.
`metapipeline_final_output_dir`	string	Absolute path for the final output directory of metapipeline-DNA that's expected to contain the output BAM from align-DNA. WARNING: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage.
`metapipeline_states_to_delete`	list	List of states for which to delete input BAMs. WARNING: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage.
`cache_intermediate_pipeline_steps`	boolean	Enable process caching from Nextflow.
`ucla_cds`	boolean	Overwrite default memory and CPU values by cluster-specific configs.
`docker_container_registry`	string	Registry containing tool Docker images.
`docker_image_gatk`, `gatk_version`	string	Docker image name and version for GATK.
`docker_image_pipeval`, `pipeval_version`	string	Docker image name and version for PipeVal.
`docker_image_gatk3`, `gatk3_version`	string	Docker image name and version for GATK3.
`docker_image_picard`, `picard_version`	string	Docker image name and version for Picard.
`docker_image_samtools`, `samtools_version`	string	Docker image name and version for SAMtools.
`reference_fasta_fai`, `reference_fasta_dict`	path	Index and dictionary files for the required input. Default: Matching `.fai` and `.dict` files in the same directory.
`bundle_v0_dbsnp138_vcf_gz_tbi`	path	Index file for the required input. Default: Matching `.tbi` file in the same directory.
`bundle_known_indels_vcf_gz_tbi`	path	Index file for the required input. Default: Matching `.tbi` file in the same directory.
`bundle_contest_hapmap_3p3_vcf_gz_tbi`	path	Index file for the required input. Default: Matching `.tbi` file in the same directory.
`bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi`	path	Index file for the required input. Default: Matching `.tbi` file in the same directory.

Base resource allocation updaters

To update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts. The default allocations can be found in the node-specific config files

base_resource_update {
    memory = [
        [['process_name', 'process_name2'], <multiplier for resource>],
        [['process_name3', 'process_name4'], <different multiplier for resource>]
    ]
    cpus = [
        [['process_name', 'process_name2'], <multiplier for resource>],
        [['process_name3', 'process_name4'], <different multiplier for resource>]
    ]
}

Note Resource updates will be applied in the order they're provided so if a process is included twice in the memory list, it will be updated twice in the order it's given.

Examples:

To double memory of all processes:

base_resource_update {
    memory = [
        [[], 2]
    ]
}

To double memory for run_ApplyBQSR_GATK and triple memory for run_validate_PipeVal and run_IndelRealigner_GATK:

base_resource_update {
    memory = [
        ['run_ApplyBQSR_GATK', 2],
        [['run_validate_PipeVal', 'run_IndelRealigner_GATK'], 3]
    ]
}

To double CPUs and memory for run_ApplyBQSR_GATK and double memory for run_validate_PipeVal:

base_resource_update {
    cpus = [
        ['run_ApplyBQSR_GATK', 2]
    ]
    memory = [
        [['run_ApplyBQSR_GATK', 'run_validate_PipeVal'], 2]
    ]
}