diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 40ed1c6..ae3a575 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -3,9 +3,13 @@ name: Tests on: push: branches: - - master + - main + - dev + workflow_dispatch: pull_request: branches-ignore: [] + schedule: + - cron: '0 0 30 * *' jobs: build-linux: @@ -13,7 +17,7 @@ jobs: strategy: max-parallel: 5 matrix: - python: [3.7,3.8,3.9] + python: [3.8,3.9,'3.10'] fail-fast: false @@ -26,36 +30,33 @@ jobs: - name: checkout git repo uses: actions/checkout@v2 - - name: Set up Python 3.X - uses: actions/setup-python@v2 + - name: conda/mamba + uses: mamba-org/setup-micromamba@v1 with: - python-version: ${{ matrix.python }} + micromamba-version: '1.3.1-0' + environment-file: environment.yml + create-args: | + python=${{ matrix.python }} + cache-environment: true + cache-downloads: true - - name: Add conda to system path - run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - echo $CONDA/bin >> $GITHUB_PATH - conda update ruamel_yaml - - - name: conda + - name: install package itself + shell: bash -el {0} run: | - conda install -c conda-forge mamba --quiet - mamba install -c bioconda -c conda-forge --quiet -y fastqc bwa samtools bamtools sambamba pigz - + pip install . - name: Install dependencies + shell: bash -el {0} run: | pip install coveralls pytest-cov pytest pytest-xdist - - name: install package itself - run: | - pip install . - - name: testing + shell: bash -el {0} run: | pytest -v --cov-report term-missing --cov=sequana_pipelines.quality_control - name: coveralls + shell: bash -l {0} run: | echo $COVERALLS_REPO_TOKEN coveralls --service=github diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index a13767b..435f810 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -8,32 +8,32 @@ on: jobs: build-n-publish: name: Build and publish to PyPI and TestPyPI - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 steps: - - uses: actions/checkout@master - - name: Set up Python 3.7 - uses: actions/setup-python@v1 + - uses: actions/checkout@main + - name: Set up Python 3.8 + uses: actions/setup-python@v2 with: - python-version: 3.7 + python-version: 3.8 - - name: Install package + - name: Install package run: | - pip install build + pip install build poetry - name: Build source tarball run: | rm -rf dist; - python setup.py sdist - + poetry build + - name: Publish distribution to Test PyPI - uses: pypa/gh-action-pypi-publish@master + uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ password: ${{ secrets.TEST_PYPI_API_TOKEN }} repository_url: https://test.pypi.org/legacy/ - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@master + uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..6707eac --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,33 @@ + +files: '\.(py|rst|sh)$' +fail_fast: false + +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.2.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + #- id: check-executables-have-shebangs + - id: check-ast + +- repo: https://github.com/pycqa/flake8 + rev: 6.1.0 + hooks: + - id: flake8 + args: ["-j8", "--ignore=E203,E501,W503,E722", "--max-line-length=120", "--exit-zero"] + +- repo: https://github.com/psf/black + rev: 22.10.0 + hooks: + - id: black + args: ["--line-length=120"] + exclude: E501 + +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + args: ["--profile", "black"] # solves conflicts between black and isort + diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 277de1f..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,6 +0,0 @@ -recursive-exclude * __pycache__ -recursive-exclude * *pyc -recursive-exclude * doc/wiki -recursive-include * *rules -include requirements*txt -include README.rst diff --git a/README.rst b/README.rst index f8f8cc0..2fedcbf 100644 --- a/README.rst +++ b/README.rst @@ -7,7 +7,7 @@ :alt: JOSS (journal of open source software) DOI .. image:: https://github.com/sequana/quality_control/actions/workflows/main.yml/badge.svg - :target: https://github.com/sequana/quality_control/actions/workflows + :target: https://github.com/sequana/quality_control/actions/workflows This pipeline is not maintained anymore but should be functional. It is a short-read quality control pipeline @@ -39,15 +39,15 @@ Usage :: sequana_quality_control --help - sequana_quality_control --input-directory DATAPATH + sequana_quality_control --input-directory DATAPATH -This creates a directory with the pipeline and configuration file. You will then need +This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:: cd quality_control sh quality_control.sh # for a local run -This launch a snakemake pipeline. If you are familiar with snakemake, you can +This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:: snakemake -s quality_control.rules -c config.yaml --cores 4 --stats stats.txt @@ -61,8 +61,6 @@ This pipelines requires the following executable(s): - fastqc - bwa -- kraken2 (optional) -- krona (optional) - sambamba - samtools - pigz @@ -74,7 +72,7 @@ This pipelines requires the following executable(s): Details ~~~~~~~ -This pipeline runs **quality_control** in parallel on the input fastq files (paired or not). +This pipeline runs **quality_control** in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced. @@ -82,7 +80,7 @@ Rules and configuration details ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here is the `latest documented configuration file `_ -to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. +to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. ChangeLog ~~~~~~~~~ @@ -91,9 +89,11 @@ ChangeLog ========= ==================================================================== Version Description ========= ==================================================================== -0.10.0 * add missing MANIFEST +0.11.0 * switch to click, pyproject. remove kraken (see multitax pipeline + instead) +0.10.0 * add missing MANIFEST 0.9.0 * remove design_file for cutadapt to reflect changes in - sequana 0.12.0 + sequana 0.12.0 * update kraken rules to use a kraken2 version * Update to use new sequana framework (0.12) * added CI action diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..700182a --- /dev/null +++ b/environment.yml @@ -0,0 +1,19 @@ +name: mapper + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - bwa + - samtools + - pigz + - fastqc + - sambamba + - pip: + - sequana + - cutadapt + - atropos + + diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..c578fce 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Libraries :: Python Modules", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Information Analysis", +] + +packages = [ + {include = "sequana_pipelines"} +] + + +[tool.poetry.dependencies] +python = ">=3.8,<4.0" +sequana = ">=0.16.4" +sequana_pipetools = ">=0.16.6" +click-completion = "^0.5.2" +click = "^8.1.7" +rich-click = "^1.7.2" +cutadapt = "^4.6" +pyproject-toml = "^0.0.10" +atropos = "^1.1.32" + + + +[tool.poetry.scripts] +sequana_quality_control = "sequana_pipelines.quality_control.main:main" + + +[tool.poetry.group.dev.dependencies] +black = "^23.7.0" +pytest = "^7.4.0" +mock = "^5.1.0" +pytest-mock = "^3.11.1" +pytest-cov = "^4.1.0" + diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 1f81455..0000000 --- a/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -sequana_pipetools>=0.7.3 -sequana>=0.12.4 -cutadapt -atropos diff --git a/sequana_pipelines/quality_control/cluster_config.json b/sequana_pipelines/quality_control/cluster_config.json deleted file mode 100644 index c9988c6..0000000 --- a/sequana_pipelines/quality_control/cluster_config.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "__default__" : - { - "ram" : "8G" - }, - - "kraken" : - { - "ram" : "16G" - } -} - - - - diff --git a/sequana_pipelines/quality_control/config.yaml b/sequana_pipelines/quality_control/config.yaml index ccb7a0c..0a03c2f 100644 --- a/sequana_pipelines/quality_control/config.yaml +++ b/sequana_pipelines/quality_control/config.yaml @@ -9,14 +9,15 @@ input_directory: /home/cokelaer/Data/Hm2 input_readtag: _R[12]_ input_pattern: '*fastq.gz' +reference_file: phiX174.fa -# if files are required for a pipeline and are within sequana or should -# be downloaded before the pipeline provide them in this section -# Note that sequana and url fields are followed by itemised files or links -# using the front dashes -requirements: - - phiX174.fa +apptainers: + pigz: https://zenodo.org/record/7346805/files/pigz_2.4.0.img + fastqc: https://zenodo.org/record/7015004/files/fastqc_0.11.9-py3.img + bwa: https://zenodo.org/record/7970243/files/bwa_0.7.17.img + graphviz: https://zenodo.org/record/7928262/files/graphviz_7.0.5.img + sequana_tools: https://zenodo.org/record/7963917/files/sequana_tools_0.15.1.img ############################################################################# # BWA used to remove a contaminant @@ -33,7 +34,6 @@ requirements: # - threads: number of threads to be used bwa_mem_phix: do: true - reference_file: phiX174.fa index_algorithm: is options: -T 30 threads: 4 @@ -72,7 +72,6 @@ bwa_mem_phix: # tool_choice__ = ["atropos", "cutadapt"] cutadapt: do: true - tool_choice: cutadapt fwd: '' rev: '' m: 20 @@ -108,20 +107,5 @@ fastqc: do_after_adapter_removal: true -################################################################# -# For taxonomy. Used in quality_control pipeline -# -# :Parameters: -# -# - do: if unchecked, this rule is ignored -# - kraken_databases: a list of databases (full path) -# Please see sequana documentation for details -# -kraken: - do: false - threads: 4 - databases: - - your_full_path_to_valid_kraken_DB - fastq_stats: max_reads: 500000 diff --git a/sequana_pipelines/quality_control/main.py b/sequana_pipelines/quality_control/main.py index 46e2626..322631f 100755 --- a/sequana_pipelines/quality_control/main.py +++ b/sequana_pipelines/quality_control/main.py @@ -10,132 +10,92 @@ # documentation: http://sequana.readthedocs.io # ############################################################################## -import sys import os -import argparse -import subprocess +import shutil +import sys +from pathlib import Path -from sequana_pipetools.options import * -from sequana_pipetools.options import before_pipeline -from sequana_pipetools.misc import Colors -from sequana_pipetools.info import sequana_epilog, sequana_prolog +import click_completion +import rich_click as click from sequana_pipetools import SequanaManager +from sequana_pipetools.options import * -col = Colors() - -NAME = "quality_control" - - -class Options(argparse.ArgumentParser): - def __init__(self, prog=NAME, epilog=None): - usage = col.purple(sequana_prolog.format(**{"name": NAME})) - super(Options, self).__init__( - usage=usage, - prog=prog, - description="", - epilog=epilog, - formatter_class=argparse.ArgumentDefaultsHelpFormatter, - ) - - # add a new group of options to the parser - so = SlurmOptions() - so.add_options(self) +import sequana_pipelines.quality_control.data - # add a snakemake group of options to the parser - so = SnakemakeOptions(working_directory=NAME) - so.add_options(self) +click_completion.init() - so = InputOptions() - so.add_options(self) +NAME = "quality_control" - so = GeneralOptions() - so.add_options(self) - pipeline_group = self.add_argument_group("pipeline") - pipeline_group.add_argument("--skip-phix-removal", action="store_true", help="Do no remove the Phix") - pipeline_group.add_argument("--skip-fastqc-raw", action="store_true", help="Do not perform fastqc on raw data") - pipeline_group.add_argument( - "--skip-fastqc-cleaned", action="store_true", help="Do not perform fastqc on cleaned data" - ) +help = init_click( + NAME, + groups={ + "Pipeline Specific": [ + "--skip-phix-removal", + "--skip-fastqc-raw", + "--skip-fastqc-cleaned", + ], + }, +) + + +@click.command(context_settings=help) +@include_options_from(ClickSnakemakeOptions, working_directory=NAME) +@include_options_from(ClickSlurmOptions) +@include_options_from(ClickInputOptions) +@include_options_from(ClickGeneralOptions) +@include_options_from(ClickTrimmingOptions, software=["cutadapt", "atropos"]) +@click.option("--skip-phix-removal", is_flag=True, help="Do no remove the Phix") +@click.option("--skip-fastqc-raw", is_flag=True, help="Do not perform fastqc on raw data") +@click.option("--skip-fastqc-cleaned", is_flag=True, help="Do not perform fastqc on cleaned data") +def main(**options): - so = TrimmingOptions(software=["cutadapt", "atropos"]) - so.software_default = "cutadapt" - so.add_options(self) + manager = SequanaManager(options, NAME) + manager.setup() - so = KrakenOptions() - so.add_options(self) + options = manager.options - # others - self.add_argument("--run", default=False, action="store_true", help="execute the pipeline directly") + cfg = manager.config.config + # fill the config file with input parameters -def main(args=None): + # --------------------------------------------------- input section + cfg.input_directory = os.path.abspath(options.input_directory) + cfg.input_pattern = options.input_pattern + cfg.input_readtag = options.input_readtag - if args is None: - args = sys.argv + # --------------------------------------------------------- trimming + cfg.trimming.software_choice = options.trimming_software_choice + cfg.trimming.do = not options.disable_trimming + qual = options.trimming_quality - # whatever needs to be called by all pipeline before the options parsing - before_pipeline(NAME) + if options.trimming_software_choice in ["cutadapt", "atropos"]: + cfg.cutadapt.tool_choice = options.trimming_software_choice + cfg.cutadapt.fwd = options.trimming_adapter_read1 + cfg.cutadapt.rev = options.trimming_adapter_read2 + cfg.cutadapt.m = options.trimming_minimum_length + cfg.cutadapt.mode = options.trimming_cutadapt_mode + cfg.cutadapt.options = options.trimming_cutadapt_options # trim Ns -O 6 + cfg.cutadapt.quality = 30 if qual == -1 else qual - # option parsing including common epilog - options = Options(NAME, epilog=sequana_epilog).parse_args(args[1:]) + # -------------------------------------------------- bwa section + cfg.bwa_mem_phix.do = not options.skip_phix_removal - # the real stuff is here - manager = SequanaManager(options, NAME) + # copy required file (possibly) + p = Path(sequana_pipelines.quality_control.data.__path__[0]) + phix = str(p / "phiX174.fa") + shutil.copy(phix, manager.workdir) - # create the beginning of the command and the working directory - manager.setup() + if options.skip_fastqc_cleaned: + cfg.fastqc.do_after_adapter_removal = False - # fill the config file with input parameters - if options.from_project is None: - cfg = manager.config.config - - # --------------------------------------------------- input section - cfg.input_directory = os.path.abspath(options.input_directory) - cfg.input_pattern = options.input_pattern - cfg.input_readtag = options.input_readtag - - # --------------------------------------------------------- trimming - cfg.trimming.software_choice = options.trimming_software_choice - cfg.trimming.do = not options.disable_trimming - qual = options.trimming_quality - - if options.trimming_software_choice in ["cutadapt", "atropos"]: - cfg.cutadapt.tool_choice = options.trimming_software_choice - cfg.cutadapt.fwd = options.trimming_adapter_read1 - cfg.cutadapt.rev = options.trimming_adapter_read2 - cfg.cutadapt.m = options.trimming_minimum_length - cfg.cutadapt.mode = options.trimming_cutadapt_mode - cfg.cutadapt.options = options.trimming_cutadapt_options # trim Ns -O 6 - cfg.cutadapt.quality = 30 if qual == -1 else qual - - # -------------------------------------------------- bwa section - cfg.bwa_mem_phix.do = not options.skip_phix_removal - - # ------------------------------------- kraken - if options.skip_kraken is True: - cfg.kraken.do = False - else: - cfg.kraken.do = True - - if options.kraken_databases: - cfg.kraken.databases = [os.path.abspath(x) for x in options.kraken_databases] - for this in options.kraken_databases: - manager.exists(this) - - if options.skip_fastqc_cleaned: - cfg.fastqc.do_after_adapter_removal = False - - if options.skip_fastqc_raw: - cfg.fastqc.do_raw = False + if options.skip_fastqc_raw: + cfg.fastqc.do_raw = False # finalise the command and save it; copy the snakemake. update the config # file and save it. manager.teardown() - if options.run: - subprocess.Popen(["sh", "{}.sh".format(NAME)], cwd=options.workdir) - if __name__ == "__main__": main() diff --git a/sequana_pipelines/quality_control/quality_control.rules b/sequana_pipelines/quality_control/quality_control.rules index 0e29a65..e295563 100644 --- a/sequana_pipelines/quality_control/quality_control.rules +++ b/sequana_pipelines/quality_control/quality_control.rules @@ -47,9 +47,6 @@ if manager.config.bwa_mem_phix.do: if manager.config.fastqc.do_after_adapter_removal: expected_output += expand("{sample}/fastqc_trimmed/fastqc.done", sample=manager.samples) -if manager.config.kraken.do: - expected_output += expand("{sample}/kraken/kraken/kraken.html", sample=manager.samples) - expected_output += expand("{sample}/kraken/kraken/kraken.json", sample=manager.samples) rule pipeline: input: ".sequana/rulegraph.svg", @@ -66,12 +63,6 @@ if manager.config.cutadapt.tool_choice == "atropos": "to a value greater than one") raise Exception -if manager.config.kraken.do is True: - if manager.config.kraken.databases in [[], "", None]: - print("ERROR: you must provide a kraken database path " + - " Check http://sequana.readthedocs.io/en/master/" + - "applications.html#sequana-taxonomy") - raise Exception # FASTQC on input data set @@ -87,8 +78,10 @@ if manager.config.fastqc.do_raw: config["fastqc"]["threads"] log: "logs/{sample}/fastqc_raw.log" + container: + config["apptainers"]["fastqc"] wrapper: - "main/wrappers/fastqc" + f"{manager.wrappers}/wrappers/fastqc" @@ -108,7 +101,7 @@ rule fastq_stat_samples: # Do we want to remove the Phix ? if manager.config.bwa_mem_phix.do: - __copy_ref__input = config["bwa_mem_phix"]["reference_file"] + __copy_ref__input = config["reference_file"] __copy_ref__output = "reference/" + os.path.basename(__copy_ref__input) rule copy_reference: @@ -133,8 +126,10 @@ if manager.config.bwa_mem_phix.do: options="", index_algorithm='is' threads: 2 + container: + config["apptainers"]["sequana_tools"] wrapper: - "main/wrappers/bwa/build" + f"{manager.wrappers}/wrappers/bwa/build" rule bwa: input: @@ -150,35 +145,70 @@ if manager.config.bwa_mem_phix.do: options=config["bwa_mem_phix"]["options"], tmp_directory=config["bwa_mem_phix"]["tmp_directory"] threads: 2 + container: + config["apptainers"]["sequana_tools"] wrapper: - "main/wrappers/bwa/align" - + f"{manager.wrappers}/wrappers/bwa/align" - __bwa_bam_to_fastq__input = "{sample}/bwa/{sample}.sorted.bam" if manager.paired is True: - _params = {"sample": manager.sample} + __bwa_bam_to_fastq__fastq_output_gz = [ + "{sample}/bwa_bam_to_fastq/{sample}_R1_.unmapped.fastq.gz", + "{sample}/bwa_bam_to_fastq/{sample}_R1_.mapped.fastq.gz", + "{sample}/bwa_bam_to_fastq/{sample}_R2_.unmapped.fastq.gz", + "{sample}/bwa_bam_to_fastq/{sample}_R2_.mapped.fastq.gz"] __bwa_bam_to_fastq__fastq_output = [ - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R1_.unmapped.fastq.gz" % _params, - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R1_.mapped.fastq.gz" % _params, - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R2_.unmapped.fastq.gz" % _params, - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R2_.mapped.fastq.gz" % _params] + "{sample}/bwa_bam_to_fastq/{sample}_R1_.unmapped.fastq", + "{sample}/bwa_bam_to_fastq/{sample}_R1_.mapped.fastq", + "{sample}/bwa_bam_to_fastq/{sample}_R2_.unmapped.fastq", + "{sample}/bwa_bam_to_fastq/{sample}_R2_.mapped.fastq"] else: + __bwa_bam_to_fastq__fastq_output_gz = [ + "{sample}/bwa_bam_to_fastq/{sample}_R1_.unmapped.fastq.gz", + "{sample}/bwa_bam_to_fastq/{sample}_R1_.mapped.fastq.gz"] __bwa_bam_to_fastq__fastq_output = [ - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R1_.unmapped.fastq.gz" % {"sample":manager.sample}, - "%(sample)s/bwa_bam_to_fastq/%(sample)s_R1_.mapped.fastq.gz" % {"sample":manager.sample}] + "{sample}/bwa_bam_to_fastq/{sample}_R1_.unmapped.fastq", + "{sample}/bwa_bam_to_fastq/{sample}_R1_.mapped.fastq" ] - __bwa_bam_to_fastq__stats_output = "%s/bwa_bam_to_fastq/bwa_mem_stats.json" % manager.sample - __bwa_bam_to_fastq__wkdir = "%s/bwa_bam_to_fastq" % manager.sample + __bwa_bam_to_fastq__stats_output = "{sample}/bwa_bam_to_fastq/bwa_mem_stats.json" + __bwa_bam_to_fastq__wkdir = "{sample}/bwa_bam_to_fastq" + + + rule bwa_bam_to_fastq: + input: + bam="{sample}/bwa/{sample}.sorted.bam" + output: + fastq=__bwa_bam_to_fastq__fastq_output, + stats=__bwa_bam_to_fastq__stats_output + params: + wkdir = __bwa_bam_to_fastq__wkdir + run: + # save some stats for later + from sequana.tools import StatsBAM2Mapped + stats = StatsBAM2Mapped(input["bam"], wkdir=params.wkdir) + stats.to_json(output["stats"]) + + rule compress_phix: + input: + fastq=rules.bwa_bam_to_fastq.output.fastq, + output: + fastq=__bwa_bam_to_fastq__fastq_output_gz, + threads: + 4 + container: + config['apptainers']['pigz'] + shell: + """ + pigz -p {threads} -f {input.fastq} + """ - include: sm.modules['bwa_bam_to_fastq'] # Run a FASTQC on the data without phix if manager.config.fastqc.do_after_phix_removal: - __fastqc_phix__input_fastq = [x for x in __bwa_bam_to_fastq__fastq_output if "unmapped" not in x] + __fastqc_phix__input_fastq = [x for x in __bwa_bam_to_fastq__fastq_output_gz if "unmapped" not in x] rule fastqc_phix: input: __fastqc_phix__input_fastq - output: + output: done="{sample}/fastqc_phix/fastqc.done" params: options=config['fastqc']["options"], @@ -187,13 +217,16 @@ if manager.config.bwa_mem_phix.do: threads= config["fastqc"]["threads"], log: "logs/{sample}/fastqc_phix.log" + container: + config["apptainers"]["fastqc"] wrapper: "main/wrappers/fastqc" rule fastq_stat_phix: - input: __bwa_bam_to_fastq__fastq_output + input: + rules.compress_phix.output.fastq output: json="{sample}/fastq_stats_phix/{sample}.json", gc="{sample}/fastq_stats_phix/{sample}_gc.png", @@ -220,7 +253,7 @@ if manager.config['trimming']['do']: if adapter_tool in ["cutadapt", "atropos"]: adapter_tool = "cutadapt" if manager.config.bwa_mem_phix.do: - __cutadapt__input_fastq = [x for x in __bwa_bam_to_fastq__fastq_output + __cutadapt__input_fastq = [x for x in __bwa_bam_to_fastq__fastq_output_gz if "unmapped" in x] __cutadapt__output = [x.replace("bwa_bam_to_fastq", "cutadapt").replace("unmapped","cutadapt") @@ -237,17 +270,130 @@ if manager.config['trimming']['do']: __cutadapt__output = [ "{sample}/cutadapt/{sample}_R1_.cutadapt.fastq.gz"] - __cutadapt__wkdir = "%s/cutadapt" % manager.sample - - # Set the fwd and rev adapters - __cutadapt__fwd = manager.config.cutadapt.fwd - __cutadapt__rev = manager.config.cutadapt.rev - - __cutadapt__options = manager.config.cutadapt.options - __cutadapt__mode = manager.config.cutadapt.mode - __cutadapt__log = "%s/logs/cutadapt/cutadapt.txt" % manager.sample - __cutadapt__sample = manager.sample - include: sm.modules["cutadapt"] + rule cutadapt: + input: + fastq = __cutadapt__input_fastq + output: + fastq = __cutadapt__output + params: + fwd = manager.config.cutadapt.fwd, + rev = manager.config.cutadapt.rev, + m = config['cutadapt']['m'], # cutoff + quality = config['cutadapt']['quality'], + kwargs = manager.config.cutadapt.options, + mode = manager.config.cutadapt.mode, + wkdir = "{sample}/cutadapt", + sample = "{sample}", + threads: + config['cutadapt']['threads'] + log: "{sample}/logs/cutadapt/cutadapt.txt" + run: + executable = config['cutadapt']['tool_choice'] # could be cutadapt or atropos + + # Fill the fwd and revcomp variables depending on the config file + fwd = params.fwd + revcomp = params.rev + + # For atropos, output must be txt AND json for the module to work. + # + # Paired data + if len(input.fastq) == 2: + if executable == "atropos": + cmd = "%s trim" % executable + cmd += " -pe1 {input.fastq[0]} -pe2 {input.fastq[1]} " + # atropos requires at least 2 threads + if int(threads) > 1: + cmd += " -T {threads} " + cmd += " --process-timeout 600 " + logpath = log[0].replace(".txt", "") + cmd += " --report-formats json txt --report-file %s" % logpath + else: + cmd = "{}".format(executable) + mode2 = params.mode.upper() + + if fwd: + cmd += " -{params.mode} %s " % fwd + else: + cmd += " -{params.mode} XXXX " + + if revcomp: + cmd += " -%s %s " % (mode2, revcomp) + else: + cmd += " -%s XXXX " % mode2 + + cmd += " -m {params.m} -q {params.quality} " + # -o is common to atropos and cutadapt for the output R1 and -p for + # R2 + cmd += " {params.kwargs} -o {output.fastq[0]} -p {output.fastq[1]}" + + # input of cutdapt must be at the end. earlier version handled + # mixing of optional arguments and positional argument but not + # latest version. In any case, it is safer to do it correctly + # (changes sequana 0.8) + if executable == "cutadapt": + cmd += " {input.fastq[0]} {input.fastq[1]} " + cmd += "> {log}" + shell(cmd) + else: + if executable == "atropos": + cmd = "%s trim -se {input.fastq[0]} " % executable + # atropos requires at least 2 threads + + if int(threads) > 1: + cmd += " -T {threads} " + cmd += " --process-timeout 600 " + logpath = log[0].replace(".txt", "") + cmd += " --report-formats json txt --report-file %s" % logpath + else: + cmd = "%s" % executable + + if fwd: + cmd += " -{params.mode} %s " % fwd + else: + cmd += " -{params.mode} XXXX " + cmd += " -m {params.m} -q {params.quality} " + cmd += " {params.kwargs} -o {output.fastq[0]}" + if executable == "cutadapt": + cmd += " {input.fastq[0]} " + cmd += " > {log}" + shell(cmd) + + elif adapter_tool in ['fastp']: + __clean_fastq__output = ["{sample}/fastp/{sample}_R1_.fastp.fastq.gz"] + if manager.paired: + __clean_fastq__output += ["{sample}/fastp/{sample}_R2_.fastp.fastq.gz"] + + _quality = config["fastp"].get("quality", 15) + _minlen = config["fastp"].get("minimum_length", 20) + + options_fastp = config["fastp"].get("options", "") + options_fastp += f" --qualified_quality_phred {_quality}" + options_fastp += f" -l {_minlen}" + if config["fastp"].get("disable_adapter_trimming", False) is True: + options_fastp += "--disable_adapter_trimming" + if config["fastp"].get("disable_quality_filtering", False) is True: + options_fastp += "--disable_quality_filtering" + + rule fastp: + input: + sample=manager.getrawdata() + output: + trimmed=__clean_fastq__output, + html="{sample}/fastp/fastp_{sample}.html", + json="{sample}/fastp/fastp_{sample}.json", # must be named fastp + log: + "logs/fastp/{sample}.log" + params: + options=config['fastp']["options"], + adapters=config["fastp"]["adapters"] + threads: + config["fastp"].get("threads", 4) + resources: + **config['fastp']['resources'] + container: + config['apptainers']['fastp'] + wrapper: + f"{manager.wrappers}/wrappers/fastp" else: raise ValueError("trimming must be either cutadapt or atropos or skewer") @@ -265,39 +411,7 @@ if manager.config['trimming']['do']: log: "logs/{sample}/fastqc_trimmed.log" wrapper: - "main/wrappers/fastqc" - - -if manager.config.kraken.do: - if manager.config['cutadapt'].do: - # todo: handle all adapter removal cases - __kraken__input = __cutadapt__output - elif manager.config.bwa_mem_phix.do: - __kraken__input = [x for x in __bwa_bam_to_fastq__fastq_output if "unmapped" in x] - else: - __kraken__input = __data__input - - __kraken__output_wkdir = manager.sample + "/kraken/" - __kraken__output_html = __kraken__output_wkdir + "kraken/kraken.html" - __kraken__output_out = __kraken__output_wkdir + "kraken/kraken.out" - __kraken__output_csv = __kraken__output_wkdir + "kraken/kraken.csv" - __kraken__output_json = __kraken__output_wkdir + "kraken/kraken.json" - - include: sm.modules["kraken/2.0"] - - - -# ====================================================================== rulegraph -sequana_rulegraph_mapper = { - "fastqc_raw": "../fastqc_raw.html", - "fastqc_phix": "../fastqc_phix.html", - "fastqc_trimmed": "../fastqc_trimmed.html", - "cutadapt": "../cutadapt.html", - "kraken": "../kraken/kraken/kraken.html", - "kraken_translate": "../kraken/raken/kraken.html", - "kraken_to_krona": "../kraken/kraken/kraken.html", - } -include: sm.modules['rulegraph'] + f"{manager.wrappers}/wrappers/fastqc" @@ -307,7 +421,7 @@ if manager.config['cutadapt'].do: # todo: handle all adapter removal cases __summary_pipeline__outputs = [ __cutadapt__output ] elif manager.config.bwa_mem_phix.do: - __summary_pipeline__outputs = [x for x in __bwa_bam_to_fastq__fastq_output if "unmapped" in x] + __summary_pipeline__outputs = [x for x in __bwa_bam_to_fastq__fastq_output_gz if "unmapped" in x] else: __summary_pipeline__outputs = [] @@ -323,7 +437,72 @@ __summary_pipeline__snakefile = str(manager.snakefile) __summary_pipeline__config = "config.yaml" __summary_pipeline__name = "Quality Control" __summary_pipeline__json_output = "{sample}/summary_pipeline/{sample}.json" -include: sm.modules["summary_pipeline"] + +rule summary: + input: + inputs = __summary_pipeline__inputs, + outputs = __summary_pipeline__outputs, + html = __summary_pipeline__html, + rulegraph = __summary_pipeline__rulegraph, + snakefile = __summary_pipeline__snakefile, + config = __summary_pipeline__config, + requirements = __summary_pipeline__requirements + output: + json = __summary_pipeline__json_output + params: + name = __summary_pipeline__name + run: + import json + import os.path + + # use real path + inputs = [os.path.realpath(f) for f in input['inputs']] + outputs = [os.path.realpath(f) for f in input['outputs']] + html = [os.path.realpath(f) for f in input['html']] + # create json + summary = {'tool': 'sequana_summary', + 'inputs': inputs, + 'outputs': outputs, + 'html': html, + 'rulegraph': os.path.realpath(input['rulegraph']), + 'requirements': os.path.realpath(input['requirements']), + 'snakefile': os.path.realpath(input['snakefile']), + 'config': os.path.realpath(input['config']), + 'name': params['name']} + js = json.dumps(summary, indent=4, sort_keys=True) + with open(output['json'], 'w') as fp: + fp.write(js) + +# ========================================================== rulegraph +sequana_rulegraph_mapper = { + "fastqc_raw": "../fastqc_raw.html", + "fastqc_phix": "../fastqc_phix.html", + "fastqc_trimmed": "../fastqc_trimmed.html", + "cutadapt": "../cutadapt.html", + "kraken": "../kraken/kraken/kraken.html", + "kraken_translate": "../kraken/raken/kraken.html", + "kraken_to_krona": "../kraken/kraken/kraken.html", + } +rule rulegraph: + input: str(manager.snakefile) + output: + svg = "rulegraph/rulegraph.dot" + params: + mapper = sequana_rulegraph_mapper, + configname = "config.yaml" + wrapper: + f"{manager.wrappers}/wrappers/rulegraph" + + +rule dot2svg: + input: + "rulegraph/rulegraph.dot" + output: + ".sequana/rulegraph.svg" + container: + config['apptainers']['graphviz'] + shell: + """dot -Tsvg {input} -o {output}""" # Those rules takes a couple of seconds so no need for a cluster @@ -333,11 +512,11 @@ localrules: rulegraph onsuccess: from sequana.modules_report.fastq_stats import FastQStatsModule from sequana.modules_report.bwa_bam_to_fastq import BWABAMtoFastQModule - from sequana.modules_report.kraken import KrakenModule from sequana.modules_report.phix import PhixModule from sequana.modules_report.cutadapt import CutadaptModule from sequana.modules_report.fastqc import FastQCModule - from sequana.modules_report.summary import SummaryModule + from sequana.modules_report.summary import SequanaReport + import json # the stats image #snake_parser = snakemake.get_argument_parser().parse_args() @@ -384,7 +563,6 @@ onsuccess: # the phix section --------------------------------- if manager.config.bwa_mem_phix.do : - print(proj) phixmod = PhixModule(proj) sample_summary["phix_section_json"] = json.loads(phixmod._get_stats().to_json()) sample_summary["phix_section"] = phixmod._get_summary() @@ -410,18 +588,6 @@ onsuccess: "content": html }) - # The Kraken section - if manager.config.kraken.do: - krakenmod = KrakenModule(proj + "/kraken/kraken") - sample_summary['kraken_json'] = json.loads(krakenmod._get_stats().to_json()) - conf.summary_sections.append({ - "name": "Kraken ", - "anchor'": "kraken", - "content": krakenmod._get_summary_section() - }) - logger.info("Copying files") - shell('cp -r %s/kraken/ %s' % (proj, report_dir)) - # The cutadapt report (independent) if manager.config['cutadapt'].do: from sequana.modules_report.cutadapt import CutadaptModule @@ -443,14 +609,14 @@ onsuccess: config.get('datatype', "unspecified"), "quality_control", __summary_pipeline__name) - SummaryModule(json.loads(open(filename).read()), intro=intro) + + SequanaReport(json.loads(open(filename).read()), intro=intro) # save sample summary sample_summary['project'] = proj with open(report_dir + "/summary.json", "w") as fp: data = json.dumps(sample_summary, indent=4, sort_keys=True) fp.write(data) - sm.create_cleanup(proj) try: logger.info("Creating multi summary file") @@ -461,11 +627,7 @@ onsuccess: except Exception as err: print(err) - - sc = sm.OnSuccessCleaner("quality_control") - sc.files_to_remove.append("phiX174.fa") - sc.add_makefile() + manager.teardown() onerror: - from sequana_pipetools.errors import PipeError - p = PipeError("quality_control") - p.status() + manager.onerror() + diff --git a/sequana_pipelines/quality_control/schema.yaml b/sequana_pipelines/quality_control/schema.yaml index c8e3b74..9819181 100644 --- a/sequana_pipelines/quality_control/schema.yaml +++ b/sequana_pipelines/quality_control/schema.yaml @@ -12,6 +12,10 @@ mapping: "input_pattern": type: str required: False + "reference_file": + type: str + required: True + pattern: .* "bwa_mem_phix": type: map @@ -19,10 +23,6 @@ mapping: "do": type: bool default: True - "reference_file": - type: str - required: True - pattern: .* "index_algorithm": type: str required: False @@ -59,18 +59,6 @@ mapping: required: True range: { min: 1 } - "kraken": - type: map - mapping: - "do": - type: bool - "threads": - type: int - required: True - range: { min: 1 } - "databases": - type: any - "fastqc": type: map @@ -89,11 +77,6 @@ mapping: required: True range: { min: 1 } - "requirements": - type: seq - sequence: - - type: str - "cutadapt": type: map mapping: diff --git a/sequana_pipelines/quality_control/requirements.txt b/sequana_pipelines/quality_control/tools.txt similarity index 72% rename from sequana_pipelines/quality_control/requirements.txt rename to sequana_pipelines/quality_control/tools.txt index 6bb5a0d..3ed1011 100644 --- a/sequana_pipelines/quality_control/requirements.txt +++ b/sequana_pipelines/quality_control/tools.txt @@ -1,8 +1,6 @@ - bwa - sambamba - samtools -- kraken2 -- ktImportText - fastqc - pigz - cutadapt diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 17c0faf..0000000 --- a/setup.cfg +++ /dev/null @@ -1,13 +0,0 @@ -# a setup configuration -[build_sphinx] -source_dir = doc/source -build_dir = doc/build -all_files = 1 - - -[aliases] -test=pytest - -[tool:pytest] -# do not use --cov because it interfers with travis command -addopts= --durations=10 --verbose -n 1 --cov sequana_pipelines.quality_control --cov-report term-missing diff --git a/setup.py b/setup.py deleted file mode 100644 index de8fc08..0000000 --- a/setup.py +++ /dev/null @@ -1,71 +0,0 @@ -# License: 3-clause BSD -from setuptools import setup, find_namespace_packages - -_MAJOR = 0 -_MINOR = 10 -_MICRO = 0 -version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO) -release = '%d.%d' % (_MAJOR, _MINOR) - -metainfo = { - 'authors': {"main": ("thomas cokelaer", "thomas.cokelaer@pasteur.fr")}, - 'version': version, - 'license' : 'new BSD', - 'url' : "https://github.com/sequana/", - 'description': """A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants""" , - 'platforms' : ['Linux', 'Unix', 'MacOsX', 'Windows'], - 'keywords' : ['snakemake, NGS, sequana, denovo, assembly, short read'], - 'classifiers' : [ - 'Development Status :: 5 - Production/Stable', - 'Intended Audience :: Education', - 'Intended Audience :: End Users/Desktop', - 'Intended Audience :: Developers', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Operating System :: OS Independent', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Topic :: Software Development :: Libraries :: Python Modules', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Topic :: Scientific/Engineering :: Information Analysis', - 'Topic :: Scientific/Engineering :: Mathematics', - 'Topic :: Scientific/Engineering :: Physics'] - } - - -setup( - name = "sequana_quality_control", - version = version, - maintainer = metainfo['authors']['main'][0], - maintainer_email = metainfo['authors']['main'][1], - author = metainfo['authors']['main'][0], - author_email = metainfo['authors']['main'][1], - long_description = open("README.rst").read(), - keywords = metainfo['keywords'], - description = metainfo['description'], - license = metainfo['license'], - platforms = metainfo['platforms'], - url = metainfo['url'], - classifiers = metainfo['classifiers'], - - # package installation - packages = ["sequana_pipelines.quality_control", - "sequana_pipelines.quality_control.data"], - - install_requires = open("requirements.txt", "r").read(), - - # This is recursive include of data files - exclude_package_data = {"": ["__pycache__"]}, - package_data = { - '': ['*.yaml', "*.rules", "*.json", "requirements.txt"], - 'sequana_pipelines.quality_control.data' : ['*.*'], - }, - - zip_safe=False, - - entry_points = {'console_scripts':[ - 'sequana_quality_control=sequana_pipelines.quality_control.main:main'] - } - -) diff --git a/singularity/Makefile b/singularity/Makefile deleted file mode 100644 index 2330596..0000000 --- a/singularity/Makefile +++ /dev/null @@ -1 +0,0 @@ -sudo singularity build sequana_quality_control.img Singularity diff --git a/singularity/Singularity b/singularity/Singularity deleted file mode 100644 index 5625936..0000000 --- a/singularity/Singularity +++ /dev/null @@ -1,23 +0,0 @@ -Bootstrap: localimage -From: sequana.img - -%labels - Author thomas cokelaer - Version v1.0 - -%post - - export PATH=$PATH:/usr/local/anaconda/bin - export LANG=C # prevents perl for raising warnings - export PERL5LIB=/usr/local/anaconda/lib/perl5/5.22.0 - - pip install sequana_quality_control - -%runscript - echo "Welcome to sequana quality_control pipeline" - exec sequana_pipelines_quality_control --version - exec sequana_pipelines_quality_control "$@" - - - - diff --git a/test/test_main.py b/test/test_main.py index 385323f..c7a3810 100644 --- a/test/test_main.py +++ b/test/test_main.py @@ -1,8 +1,11 @@ -import easydev import os -import tempfile import subprocess import sys +import tempfile + +from click.testing import CliRunner + +from sequana_pipelines.quality_control.main import main from . import test_dir @@ -15,16 +18,19 @@ def test_standalone_subprocess(): directory = tempfile.TemporaryDirectory() cmd = """sequana_quality_control --input-directory {} - --working-directory --force""".format(sharedir, directory.name) + --working-directory --force""".format( + sharedir, directory.name + ) subprocess.call(cmd.split()) def test_standalone_script(): directory = tempfile.TemporaryDirectory() - import sequana_pipelines.quality_control.main as m - sys.argv = ["test", "--input-directory", sharedir, "--working-directory", - directory.name, "--force", "--skip-kraken"] - m.main() + args = ["--input-directory", sharedir, "--working-directory", directory.name, "--force"] + runner = CliRunner() + results = runner.invoke(main, args) + assert results.exit_code == 0 + def test_full(): @@ -33,7 +39,7 @@ def test_full(): wk = directory cmd = "sequana_quality_control --input-directory {} " - cmd += "--working-directory {} --force --skip-kraken " + cmd += "--working-directory {} --force " cmd = cmd.format(sharedir, wk) subprocess.call(cmd.split()) @@ -41,7 +47,7 @@ def test_full(): assert os.path.exists(wk + "/summary.html") + def test_version(): cmd = "sequana_quality_control --version" subprocess.call(cmd.split()) -