input.BAM |
yes |
path |
BAM file for which to calculate coverage, path provided in input yaml. |
target_BED |
yes |
path |
BED file specifying target intervals (defines regions for target and off-target coverage operations). |
save_intermediate_files |
yes |
boolean |
Whether to save intermediate files. |
reference_dict |
yes |
path |
Human genome reference dictionary file for use in BED to INTERVAL_LIST conversion. Required if collecting metrics. |
reference_dbSNP |
yes |
path |
dbSNP reference VCF file, with proper chromosome encoding and compression. See discussion. Required if performing off-target read depth calculation. |
genome_sizes |
yes |
path |
Reference file consisting of chromosomes and their lengths used by bedtools slop. Required for off-target read depth workflows. .fai files accepted. |
target_depth |
no |
bool |
Whether to calculate per-base read depth in targeted regions. Default false. |
off_target_depth |
no |
bool |
Whether to perform off-target read depth calculation at dbSNP loci. Default true. |
output_enriched_target_file |
no |
bool |
Whether to output a new target file containing coverage-enriched off-target dbSNP loci. Default true. |
min_read_depth |
no |
bool |
Minimum read depth threshold for an off-target locus to be considered enriched and be included in the new target file. Default 30. |
min_base_quality |
no |
integer |
Minimum base quality for a read to be counted in depth calculation by samtools depth. Applies to both off- and on-target calculations. Defaults to 20. |
min_mapping_quality |
no |
integer |
Minimum mapping quality for a read to be counted in depth calculation by samtools depth. Applies to both off- and on-target calculations. Defaults to 20. |
collect_metrics |
no |
bool |
Whether to run CollectHsMetrics. Default true. |
target_interval_list |
no |
path |
Interval list file specifying target intervals used to calculate coverage by collecHsMetrics. If not provided, the target BED will be used to calculate the intervals. |
bait_BED |
no |
path |
BED file with bait locations that can be used to generate a bait interval list used by CollecHsMetrics. If not provided, the target BED will be used. |
bait_interval_list |
no |
path |
Interval list file specifying bait intervals used by CollectHsMetrics. If not provided, the bait BED will be used to calculate the intervals. |
save_interval_list |
yes |
boolean |
Whether to save a copy of any generated interval lists. Saves to the output_dir. |
save_all_dbSNP |
no |
boolean |
Whether to save a copy of the read depth BED file for all dbSNP loci generated by the off-target workflows. Default false. |
save_raw_target_bed |
no |
boolean |
Whether to save a copy of the per-base, target read depth BED with uncollapsed intervals. Default false. |
off_target_slop |
no |
integer |
Number of base pairs to add to either side of target file coordinates so that they may be excluded from off-target read depth calculation. Default is 500. |
dbSNP_slop |
no |
integer |
Number of base pairs to add to either side of off-target dbSNP loci to generate off-target intervals. The purpose is to merge adjacent dbSNP loci into single intervals prior to mergeing with target intervals. Default is 150. |
coverage_cap |
no |
integer |
COVERAGE_CAP parameter for CollectHsMetrics, determines the coverage threshold at which to stop calculating coverage. |
near_distance |
no |
integer |
NEAR_DISTANCE parameter for CollectHsMetrics, determines the maximum distance in bp of a read from the nearest probe (bait) for it to be counted as "near probe" in metrics calculations. Default 250. |
samtools_depth_extra_args |
no |
string |
Extra arguments for samtools depth. |
picard_CollectHsMetrics_extra_args |
no |
string |
Extra arguments for picard CollectHsMetrics. |
merge_operation |
no |
string |
Operation performed on read depth column values when intervals are collapsed during bedtools merge. Defaults to 'collapse'. See bedtools documentation for other options. |
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. |