index_ref_bwa | R Documentation |
This function indexes a reference genome using the bwa aligner
index_ref_bwa(
bin_bwa = build_default_tool_binary_list()$bin_bwa,
file = "",
threads = 4,
ram = 4,
verbose = FALSE,
batch_config = build_default_preprocess_config(),
executor_id = make_unique_id("refIndex"),
task_name = "refIndex",
mode = "local",
time = "48:0:0",
update_time = 60,
wait = FALSE,
hold = NULL
)
bin_bwa |
Path to bwa executable. Default path tools/bwa/bwa. |
file |
Path to the input file with the reference genome in FASTA format. |
verbose |
Enables progress messages. Default False. |
executor_id |
Task EXECUTOR ID. Default "refIndex" |
task_name |
Task name. Default "refIndex" |
mode |
REQUIRED Where to parallelize. Default local. Options "local","batch" |
time |
OPTIONAL If batch mode. Max run time per job. Default "48:0:0" |
update_time |
OPTIONAL If batch mode. Job update time in seconds. Default 60. |
wait |
OPTIONAL If batch mode wait for batch to finish. Default FALSE |
output_dir |
Path to the output directory. |
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