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Wrap minimap2 #128

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* add cmdline option to control total pipe_buffer usage. Limit to saf…
…e 4MB as long as we do not properly treat it as a resource
marvin-jens committed Nov 18, 2024
commit f5000f49e4f53901d3383efcd5281dc2bc9fb20a
9 changes: 8 additions & 1 deletion spacemake/bin/fastq_to_uBAM.py
Original file line number Diff line number Diff line change
@@ -194,7 +194,7 @@ def main(args):

# queues for communication between processes
w = (
mf.Workflow("fastq_to_uBAM",total_pipe_buffer_MB=8)
mf.Workflow("fastq_to_uBAM", total_pipe_buffer_MB=args.pipe_buffer)
# open reads2.fastq.gz
.gz_reader(inputs=input_reads2, output=mf.FIFO("read2", "wb")).distribute(
input=mf.FIFO("read2", "rt"),
@@ -365,6 +365,13 @@ def parse_args():
type=int,
help="phred quality base (default=33)",
)
parser.add_argument(
"--pipe-buffer",
default=4,
type=int,
help="How many megabytes of pipe-buffer to use. kernel settings is usually 64MB per user (default=4MB)",
)

parser.add_argument(
"--parallel", default=1, type=int, help="how many processes to spawn"
)