Inputs

Input YAML

Example:

---
patient_id: 'patient_id'
dataset_id: 'dataset_id'
input:
  normal:
    - path: /absolute/path/to/normal.bam
      read_length: length
  tumor:
    - path: /absolute/path/to/tumor.bam
      read_length: length

Config

Field	Type	Required	Description
algorithm	list	no	List of tools to be run: ['fastqc', 'samtools_stats', 'collectwgsmetrics', 'collecthsmetrics', 'mosdepth_coverage', 'mosdepth_quantize', 'qualimap_bamqc'], default = ['stats', 'collectwgsmetrics']
reference	path	yes/no	Reference fasta is required only for CollectWgsMetrics and CollectHsMetrics
intervals_bed	path	no	Absolute path to BED file with intervals to process
output_dir	path	yes	Not required if blcds_registered_dataset = true
blcds_registered_dataset	boolean	no	Default is false. Only uclahs_cds users should change this. When true, BLCDS folder structure is used
work_dir	path	no	Path of working directory for Nextflow. When included, Nextflow intermediate files and logs will be saved to this directory. With uclahs_cds = true, 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.

SAMtools specific configuration

Field	Type	Required	Description
stats_max_rgs_per_sample	integer	no	If a sample has more than this number of readgroups, SAMtools stats will not run per readgroup analysis. Default = 20
stats_max_libs_per_sample	integer	no	If a sample has more than this number of libraries, SAMtools stats will not run per library analysis. Default = 20
stats_remove_duplicates	boolean	no	Ignore reads marked as duplicate. Default = false
stats_additional_options	string	no	Any additional options recognized by samtools stats

Picard CollectWgsMetrics specific configuration

Field	Type	Required	Description
cwm_coverage_cap	integer	no	Cap coverage at this value. Default = 250
cwm_minimum_mapping_quality	integer	no	Ignore reads with mapping quality below this value. Default = 20
cwm_minimum_base_quality	integer	no	Ignore bases with quality below this value. Default = 20
cwm_use_fast_algorithm	boolean	no	If true, fast algorithm is used
cwm_additional_options	string	no	Any additional options recognized by CollectWgsMetrics

Picard CollectHsMetrics specific configuration

Field	Type	Required	Description
chm_bait_intervals_bed	path	no	if not defined, intervals_bed will be used
chm_coverage_cap	integer	no	Cap coverage at this value. Default = 250
chm_minimum_mapping_quality	integer	no	Ignore reads with mapping quality below this value. Default = 20
chm_minimum_base_quality	integer	no	Ignore bases with quality below this value. Default = 20
chm_per_base_output	boolean	no	Default = false
chm_additional_options	string	no	Any additional options recognized by CollectWgsMetrics

FastQC specific configuration

Field	Type	Required	Description
fastqc_level	string	yes	'readgroup', 'library' or 'sample'
fastqc_additional_options	string	no	Any additional options recognized by FastQC

Qualimap specific configuration

Field	Type	Required	Description
bamqc_output_format	string	no	Choice of 'pdf' or 'html', default = 'html'. html is needed for multiqc
bamqc_additional_options	string	no	Any additional options recognized by bamqc

mosdepth window-based coverage specific configuration

Field	Type	Required	Description
mosdepth_windows	integer	no	Size for mosdepth windows coverage calculations. Not used if intervals_bed is defined. Default = 500
mosdepth_use_fast_algorithm	boolean	no	fast algorithm ignores read pair overlaps and CIGARs. It should not be used on libraries with small insert sizes. Default = false
mosdepth_per_base_output	boolean	no	Output coverage for every base. Default = true
mosdepth_additional_options	string	no	Any additional options recognized by mosdepth, --mapq 20 recommended

mosdepth quantize specific configuration

Field	Type	Required	Description
mosdepth_quantize_cutoffs	string	no	cutoffs for coverage regions. Default = 0:1:5:150
mosdepth_quantize_use_fast_algorithm	boolean	no	fast algorithm ignores read pair overlaps and CIGARs. It should not be used on libraries with small insert sizes. Default = false
mosdepth_q0_label	string	no	lowest coverage regions label. Default = Q0
mosdepth_q1_label	string	no	next coverage regions label. Default = Q1
mosdepth_q2_label	string	no	next coverage regions label. Default = Q2
mosdepth_q3_label	string	no	highest coverage regions label. Default = Q3
mosdepth_quantize_additional_options	string	no	Any additional options recognized by mosdepth. --mapq 20 recommended

Base resource allocation updaters

To update the base resource (cpus or memory) allocations for processes, use the following structure. 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_CollectWgsMetrics_Picard and triple memory for run_statsSamples_SAMtools and run_bamqc_Qualimap:

base_resource_update {
    memory = [
        ['run_CollectWgsMetrics_Picard', 2],
        [['run_statsSamples_SAMtools', 'run_bamqc_Qualimap'], 3]
    ]
}

• To double CPUs and memory for run_CollectWgsMetrics_Picard and double memory for run_statsSamples_SAMtools:

base_resource_update {
    cpus = [
        ['run_CollectWgsMetrics_Picard', 2]
    ]
    memory = [
        [['run_CollectWgsMetrics_Picard', 'run_statsSamples_SAMtools'], 2]
    ]
}

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