PICARD SAMTOFASTQ

Converts a SAM or BAM file to FASTQ.

URL:

Example

This wrapper can be used in the following way:

rule bam_to_fastq:
    input:
        "mapped/{sample}.bam",
    output:
        fastq1="reads/{sample}.R1.fastq",
        fastq2="reads/{sample}.R2.fastq",
    log:
        "logs/picard/sam_to_fastq/{sample}.log",
    params:
        extra="",  # optional: Extra arguments for picard.
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024,
    wrapper:
        "v1.1.0/bio/picard/samtofastq"

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.

Software dependencies

  • picard=2.26
  • snakemake-wrapper-utils==0.1.3

Input/Output

Input:

  • sam/bam file

Output:

  • fastq files.

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.
  • –TMP_DIR is automatically set by resources.tmpdir
  • For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

Authors

  • Patrik Smeds

Code

"""Snakemake wrapper for picard SortSam."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

fastq1 = snakemake.output.fastq1
fastq2 = snakemake.output.get("fastq2", None)
fastq_unpaired = snakemake.output.get("unpaired_fastq", None)

if not isinstance(fastq1, str):
    raise ValueError("f1 needs to be provided")

output = f"--FASTQ {fastq1}"

if isinstance(fastq2, str):
    output += f" --SECOND_END_FASTQ {fastq2}"

if isinstance(fastq_unpaired, str):
    if not isinstance(fastq2, str):
        raise ValueError("f2 is required if fastq_unpaired is set")

    output += f" --UNPAIRED_FASTQ {fastq_unpaired}"

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard SamToFastq"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input[0]}"
        " --TMP_DIR {tmpdir}"
        " {output}"
        " {log}"
    )