sample_name |
yes |
string |
The sample name. This is ignored if the output files are directly saved to the Boutros Lab data storage registry, by setting ucla_cds_registered_dataset_output = true |
input_csv |
yes |
path |
Absolute path to the input csv. See here for example and above for the detail of required fields. |
reference_fasta_bwa |
yes for BWA-MEM2 |
path |
Absolute path to the reference genome fasta file. The reference genome is used by BWA-MEM2 for alignment. |
reference_fasta_hisat2 |
yes for HISAT2 |
path |
Absolute path to the reference genome fasta file. The reference genome is used by HISAT2 for alignment. |
hisat2_index_prefix |
yes for HISAT2 |
path |
Absolute path up to the genome index basename. The index must be generated by the hisat2-build command. |
aligner |
yes |
list |
Which aligners to use as strings in list format. Current options: BWA-MEM2, HISAT2. |
output_dir |
yes |
path |
Absolute path to the directory where the output files to be saved. This is ignored if the output files are directly saved to the Boutros Lab data storage registry, by setting ucla_cds_registered_dataset_output = true |
save_intermediate_files |
yes |
boolean |
Save intermediate files. If yes, not only the final BAM, but also the unmerged, unsorted, and duplicates unmarked BAM files will also be saved. |
cache_intermediate_pipeline_steps |
yes |
boolean |
Enable cahcing to resume pipeline and the end of the last successful process completion when a pipeline fails (if true the default submission script must be modified). |
mark_duplicates |
no |
boolean |
Disable processes which mark duplicates. When false, the pipeline stops at the sorting step, outputting a sorted, indexed, unmerged BAM with unmarked duplicates. Recommended for high coverage targeted panel sequencing datasets. Defaults as true to mark duplicates as usual. |
enable_spark |
yes |
boolean |
Enable use of Spark processes. When true, MarkDuplicatesSpark will be used. When false, MarkDuplicates will be used. Default value is true. |
spark_temp_dir |
no |
path |
Path to temp dir for Spark processes. When included in the sample config file, Spark intermediate files will be saved to this directory. Defaults to /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. |
spark_metrics |
no |
boolean |
should Spark generate *.mark_dup.metrics |
work_dir |
no |
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. |
max_number_of_parallel_jobs |
no |
int |
The maximum number of jobs or steps of the pipeline that can be ran in parallel. Default is 1. Be very cautious setting this to any value larger than 1, as it may cause out-of-memory error. It may be helpful when running on a big memory computing node. |
bwa_mem_number_of_cpus |
no |
int |
Number of cores to use for BWA-MEM2. If not set, this will be calculated to ensure at least 2.5Gb memory per core. |
ucla_cds_registered_dataset_input |
yes |
boolean |
Input FASTQs are from the Boutros Lab data registry. |
ucla_cds_registered_dataset_output |
yes |
boolean |
Enable saving final files including BAM and BAM index, and logging files directory to the Boutros Lab Data registry. |
dataset_id |
no |
string |
The registered dataset ID of this dataset from the Boutros Lab data registry. Ignored if ucla_cds_registered_data_input = true or ucla_cds_registered_output = false |
patient_id |
no |
string |
The registered patient ID of this sample from the Boutros Lab data registry. Ignored if ucla_cds_registered_data_input = true or ucla_cds_registered_output = false |
sample_id |
no |
string |
The registered sample ID from the Boutros Lab data registry. Ignored if ucla_cds_registered_data_input = true or ucla_cds_registered_output = false |
disable_alt_aware |
yes |
boolean |
Whether to disable the default alt-aware mode for BWA-MEM2. The default behavior of alt-aware mode is to consider the .alt file if it exists in the directory with the reference file. |
ucla_cds_data_dir |
no |
string |
The directory where registered data is located. Default: /hot/data |
ucla_cds_reference_genome_version |
no |
string |
Identifier for the version of the reference genome version |
check_node_config |
no |
boolean |
Whether to check pre-configured node settings used to set CPU and memory constraints. The default behavior, whether true or undefined is to check the pre-configured node settings. Set to false to skip this check. |
docker_container_registry |
no |
string |
Registry containing tool Docker images. Default: ghcr.io/uclahs-cds |