GATK PRINTREADSSPARK¶
Write reads from SAM format file (SAM/BAM/CRAM) that pass specified criteria to a new file. This is the version that can be run on Spark.
Example¶
This wrapper can be used in the following way:
rule gatk_printreadsspark:
input:
bam="mapped/{sample}.bam",
ref="genome.fasta",
dict="genome.dict",
output:
bam="{sample}.bam",
log:
"logs/{sample}.log",
params:
extra="", # optional
java_opts="", # optional
#spark_runner="", # optional, local by default
#spark_v1.12.2="", # optional
#spark_extra="", # optional
resources:
mem_mb=1024,
threads: 8
wrapper:
"v1.12.2/bio/gatk/printreadsspark"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Notes¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments for printreadsspark.
- The spark_runner param = “LOCAL”|”SPARK”|”GCS” allows to set the spark_runner. Set the parameter to “LOCAL” or don’t set it at all to run on local machine.
- The spark_master param allows to set the URL of the Spark Master to submit the job. Set to “local[number_of_cores]” for local execution. Don’t set it at all for local execution with number of cores determined by snakemake.
- The spark_extra param allows for additional spark arguments.
- For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/360057441531-PrintReadsSpark
Software dependencies¶
gatk4=4.2
openjdk=8
snakemake-wrapper-utils=0.2
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
spark_runner = snakemake.params.get("spark_runner", "LOCAL")
spark_master = snakemake.params.get(
"spark_master", "local[{}]".format(snakemake.threads)
)
spark_extra = snakemake.params.get("spark_extra", "")
java_opts = get_java_opts(snakemake)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' PrintReadsSpark"
" --input {snakemake.input.bam}"
" --reference {snakemake.input.ref}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.bam}"
" -- --spark-runner {spark_runner} --spark-master {spark_master} {spark_extra}"
" {log}"
)