PICARD SOMTOFASTQ

Converts a SAM or BAM file to FASTQ.

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:
        "0.73.0/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==2.22.1
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• sam/bam file

Output:

• fastq files.

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"


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 = " FASTQ=" + fastq1

if isinstance(fastq2, str):
    output += " 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 += " UNPAIRED_FASTQ=" + fastq_unpaired

shell(
    "picard"
    " SamToFastq"
    " {java_opts}"
    " {extra}"
    " INPUT={snakemake.input[0]}"
    " {output}"
    " {log}"
)