DNA-seq and Neoantigens prediction

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gatk-snakemake-pipeline
gatk-snakemake-pipeline
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Snakemake workflow for neoantigen prediction.

This workflow is still in development

This snakemake pipeline implements the GATK best-practices workflow

Step 1 Clone repository

Clone this repository to your local system 需要写一个脚本判断是否有conda，如果没有自动下载安装并创建snakemake环境

Step 2 Edit files

Configure the workflow accoreding to your needs via editing the files config.yaml ， sample.tsv

Step 3 Execute the process

This workflow will download reference genomes and annotation automatically. Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores N

using N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

Step 4 Inspection results

After execution, you can create a self-contained interactive HTML report with all results via:

snakemake --report report.HTML

Code Snippets

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wrapper:
    "0.64.0/bio/bwa/mem"
SnakeMake From line 15 of GATK_pipline/mapping.smk 
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wrapper:
    "0.64.0/bio/picard/markduplicates"
SnakeMake From line 26 of GATK_pipline/mapping.smk 
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wrapper:
    "0.64.0/bio/gatk/baserecalibrator"
SnakeMake From line 41 of GATK_pipline/mapping.smk 
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wrapper:
    "0.64.0/bio/gatk/applybqsr"
SnakeMake From line 56 of GATK_pipline/mapping.smk 
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wrapper:
    "0.64.0/bio/gatk/mutect"
SnakeMake From line 16 of GATK_pipline/mutation_calling.smk 
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wrapper:
    "0.64.0/bio/fastp"
SnakeMake fastp From line 17 of GATK_pipline/qc.smk 
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wrapper:
    "0.64.0/bio/fastp"
SnakeMake fastp From line 32 of GATK_pipline/qc.smk 
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wrapper:
    "0.64.0/bio/reference/ensembl-sequence"
SnakeMake From line 13 of GATK_pipline/ref.smk 
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wrapper:
    "0.64.0/bio/bwa/index"
SnakeMake From line 26 of GATK_pipline/ref.smk 
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shell: 
    "samtools dict {input} > {output} 2 > {log}"
SnakeMake SAMtools From line 40 of GATK_pipline/ref.smk 
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wrapper:
    "0.64.0/bio/samtools/faidx"
SnakeMake From line 51 of GATK_pipline/ref.smk 
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    wrapper:
        "0.64.0/bio/vep/plugins"
'''
有一个wildtype插件需要自己下
'''
SnakeMake From line 61 of GATK_pipline/ref.smk 
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wrapper:
    "0.64.0/bio/vep/cache"
SnakeMake From line 76 of GATK_pipline/ref.smk 
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wrapper:
    "0.64.0/bio/razers3"
SnakeMake razers3 From line 12 of HLAtyping/fish_fastq.smk 
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wrapper:
    "0.64.0/bio/optitype"
SnakeMake From line 11 of HLAtyping/typing.smk 
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__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2016, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"

from os import path

from snakemake.shell import shell

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

# Check inputs/arguments.
if len(snakemake.input) == 0:
    raise ValueError("A reference genome has to be provided!")
elif len(snakemake.input) > 1:
    raise ValueError("Only one reference genome can be inputed!")

# Prefix that should be used for the database
prefix = snakemake.params.get("prefix", "")

if len(prefix) > 0:
    prefix = "-p " + prefix

# Contrunction algorithm that will be used to build the database, default is bwtsw
construction_algorithm = snakemake.params.get("algorithm", "")

if len(construction_algorithm) != 0:
    construction_algorithm = "-a " + construction_algorithm

shell(
    "bwa index" " {prefix}" " {construction_algorithm}" " {snakemake.input[0]}" " {log}"
)
Python Snakemake BWA From line 1 of index/wrapper.py 
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__author__ = "Johannes Köster, Julian de Ruiter"
__copyright__ = "Copyright 2016, Johannes Köster and Julian de Ruiter"
__email__ = "koester@jimmy.harvard.edu, julianderuiter@gmail.com"
__license__ = "MIT"


from os import path

from snakemake.shell import shell


# Extract arguments.
extra = snakemake.params.get("extra", "")

sort = snakemake.params.get("sort", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")

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

# Check inputs/arguments.
if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
    1,
    2,
}:
    raise ValueError("input must have 1 (single-end) or " "2 (paired-end) elements")

if sort_order not in {"coordinate", "queryname"}:
    raise ValueError("Unexpected value for sort_order ({})".format(sort_order))

# Determine which pipe command to use for converting to bam or sorting.
if sort == "none":

    # Simply convert to bam using samtools view.
    pipe_cmd = "samtools view -Sbh -o {snakemake.output[0]} -"

elif sort == "samtools":

    # Sort alignments using samtools sort.
    pipe_cmd = "samtools sort {sort_extra} -o {snakemake.output[0]} -"

    # Add name flag if needed.
    if sort_order == "queryname":
        sort_extra += " -n"

    prefix = path.splitext(snakemake.output[0])[0]
    sort_extra += " -T " + prefix + ".tmp"

elif sort == "picard":

    # Sort alignments using picard SortSam.
    pipe_cmd = (
        "picard SortSam {sort_extra} INPUT=/dev/stdin"
        " OUTPUT={snakemake.output[0]} SORT_ORDER={sort_order}"
    )

else:
    raise ValueError("Unexpected value for params.sort ({})".format(sort))

shell(
    "(bwa mem"
    " -t {snakemake.threads}"
    " {extra}"
    " {snakemake.params.index}"
    " {snakemake.input.reads}"
    " | " + pipe_cmd + ") {log}"
)
Python Snakemake SAMtools Picard From line 1 of mem/wrapper.py 
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__author__ = "Sebastian Kurscheid"
__copyright__ = "Copyright 2019, Sebastian Kurscheid"
__email__ = "sebastian.kurscheid@anu.edu.au"
__license__ = "MIT"

from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

n = len(snakemake.input.sample)
assert (
    n == 1 or n == 2
), "input->sample must have 1 (single-end) or 2 (paired-end) elements."

if n == 1:
    reads = "--in1 {}".format(snakemake.input.sample)
else:
    reads = "--in1 {} --in2 {}".format(*snakemake.input.sample)

trimmed_paths = snakemake.output.get("trimmed", None)
if trimmed_paths is not None:
    if n == 1:
        trimmed = "--out1 {}".format(snakemake.output.trimmed)
    else:
        trimmed = "--out1 {} --out2 {}".format(*snakemake.output.trimmed)
else:
    trimmed = ""

html = "--html {}".format(snakemake.output.html)
json = "--json {}".format(snakemake.output.json)

shell(
    "(fastp --thread {snakemake.threads} {snakemake.params.extra} "
    "{reads} "
    "{trimmed} "
    "{json} "
    "{html} ) {log}"
)
Python Snakemake JSON From line 1 of fastp/wrapper.py 
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__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"


from snakemake.shell import shell

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

log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
shell(
    "gatk --java-options '{java_opts}' ApplyBQSR {extra} -R {snakemake.input.ref} -I {snakemake.input.bam} "
    "--bqsr-recal-file {snakemake.input.recal_table} "
    "-O {snakemake.output.bam} {log}"
)
Python Snakemake gatk From line 1 of applybqsr/wrapper.py 
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__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"


from snakemake.shell import shell

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

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
known = snakemake.input.get("known", "")
if known:
    known = "--known-sites {}".format(known)

shell(
    "gatk --java-options '{java_opts}' BaseRecalibrator {extra} "
    "-R {snakemake.input.ref} -I {snakemake.input.bam} "
    "-O {snakemake.output.recal_table} {known} {log}"
)
Python Snakemake gatk From line 1 of baserecalibrator/wrapper.py 
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__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2019, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake.utils import makedirs

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

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

shell(
    "gatk Mutect2 "  # Tool and its subprocess
    "--input {snakemake.input.map} "  # Path to input mapping file
    "--output {snakemake.output.vcf} "  # Path to output vcf file
    "--reference {snakemake.input.fasta} "  # Path to reference fasta file
    "{extra} "  # Extra parameters
    "{log}"  # Logging behaviour
)
Python Snakemake gatk From line 3 of mutect/wrapper.py 
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__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"


import os
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
outdir = os.path.dirname(snakemake.output[0])

# get sequencing type
seq_type = snakemake.params.get("sequencing_type", "dna")
seq_type = "--{}".format(seq_type)

# check if non-default config.ini is used
config = snakemake.params.get("config", "")
if any(config):
    config = "--config {}".format(config)

shell(
    "(OptiTypePipeline.py"
    " --input {snakemake.input.reads}"
    " --outdir {outdir}"
    " --prefix {snakemake.wildcards.sample}"
    " {seq_type}"
    " {config}"
    " {extra})"
    " {log}"
)
Python Snakemake From line 1 of optitype/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell

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

shell(
    "picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
    "OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
    "{log}"
)
Python Snakemake Picard From line 1 of markduplicates/wrapper.py 
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__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"


import os
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


shell(
    "(razers3"
    " -tc {snakemake.threads}"
    " {extra}"
    " -o {snakemake.output[0]}"
    " {snakemake.params.genome}"
    " {snakemake.input.reads})"
    " {log}"
)
Python Snakemake From line 1 of razers3/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

import subprocess as sp
import sys
from itertools import product
from snakemake.shell import shell

species = snakemake.params.species.lower()
release = int(snakemake.params.release)
build = snakemake.params.build

branch = ""
if release >= 81 and build == "GRCh37":
    # use the special grch37 branch for new releases
    branch = "grch37/"

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

spec = ("{build}" if int(release) > 75 else "{build}.{release}").format(
    build=build, release=release
)

suffixes = ""
datatype = snakemake.params.get("datatype", "")
if datatype == "dna":
    suffixes = ["dna.primary_assembly.fa.gz", "dna.toplevel.fa.gz"]
elif datatype == "cdna":
    suffixes = ["cdna.all.fa.gz"]
elif datatype == "cds":
    suffixes = ["cds.all.fa.gz"]
elif datatype == "ncrna":
    suffixes = ["ncrna.fa.gz"]
elif datatype == "pep":
    suffixes = ["pep.all.fa.gz"]
else:
    raise ValueError("invalid datatype, must be one of dna, cdna, cds, ncrna, pep")

success = False
for suffix in suffixes:
    url = "ftp://ftp.ensembl.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}".format(
        release=release,
        species=species,
        datatype=datatype,
        spec=spec.format(build=build, release=release),
        suffix=suffix,
        species_cap=species.capitalize(),
        branch=branch,
    )

    try:
        shell("curl -sSf {url} > /dev/null 2> /dev/null")
    except sp.CalledProcessError:
        continue

    shell("(curl -L {url} | gzip -d > {snakemake.output[0]}) {log}")
    success = True
    break

if not success:
    print(
        "Unable to download requested sequence data from Ensembl. "
        "Did you check that this combination of species, build, and release is actually provided?",
        file=sys.stderr,
    )
    exit(1)
Python Snakemake From line 1 of ensembl-sequence/wrapper.py 
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__author__ = "Michael Chambers"
__copyright__ = "Copyright 2019, Michael Chambers"
__email__ = "greenkidneybean@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell


shell("samtools faidx {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]}")
Python Snakemake SAMtools From line 1 of faidx/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

from pathlib import Path
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "vep_install --AUTO cf "
    "--SPECIES {snakemake.params.species} "
    "--ASSEMBLY {snakemake.params.build} "
    "--CACHE_VERSION {snakemake.params.release} "
    "--CACHEDIR {snakemake.output} "
    "--CONVERT "
    "--NO_UPDATE {log}"
)
Python Snakemake From line 1 of cache/wrapper.py 
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

import sys
from pathlib import Path
from urllib.request import urlretrieve
from zipfile import ZipFile
from tempfile import NamedTemporaryFile

if snakemake.log:
    sys.stderr = open(snakemake.log[0], "w")

outdir = Path(snakemake.output[0])
outdir.mkdir()

with NamedTemporaryFile() as tmp:
    urlretrieve(
        "https://github.com/Ensembl/VEP_plugins/archive/release/{release}.zip".format(
            release=snakemake.params.release
        ),
        tmp.name,
    )

    with ZipFile(tmp.name) as f:
        for member in f.infolist():
            memberpath = Path(member.filename)
            if len(memberpath.parts) == 1:
                # skip root dir
                continue
            targetpath = outdir / memberpath.relative_to(memberpath.parts[0])
            if member.is_dir():
                targetpath.mkdir()
            else:
                with open(targetpath, "wb") as out:
                    out.write(f.read(member.filename))
Python From line 1 of plugins/wrapper.py
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/limbo1996/GATK-snakemake-pipeline
Name: gatk-snakemake-pipeline
Version: 1
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Copyright: Public Domain
License: None
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