PICARD SOMTOFASTQ

Converts a SAM or BAM file to FASTQ.

Software dependencies

  • picard ==2.18.16

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.
    wrapper:
        "0.30.0/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.

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


extra = snakemake.params.get("extra", "")
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")
    else:
        output += " UNPAIRED_FASTQ=" + fastq_unpaired

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