SAMTOOLS FASTX

Converts a SAM, BAM or CRAM into FASTQ or FASTA format.

Example

This wrapper can be used in the following way:

rule samtools_fastq:
    input:
        "{prefix}.sam",
    output:
        "{prefix}.fasta",
    log:
        "{prefix}.log",
    message:
        ""
    # Samtools takes additional threads through its option -@
    threads: 2  # This value - 1 will be sent to -@
    params:
        outputtype="fasta",
        extra="",
    wrapper:
        "v3.8.0/bio/samtools/fastx/"

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 extra param allows for additional program arguments (not -@/–threads or -o).

• For more information see, http://www.htslib.org/doc/samtools-fasta.html

Software dependencies

• samtools=1.19.2

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• bam or sam file (.bam, .sam)

Output:

• fastq file (.fastq) or fasta file (.fasta)

Authors

• William Rowell

• Filipe G. Vieira

Code

__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(
    snakemake, parse_write_index=False, parse_output_format=False
)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


shell(
    "samtools {snakemake.params.outputtype} {samtools_opts} {extra} {snakemake.input} {log}"
)