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‎.editorconfig‎

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# EditorConfig is awesome: http://EditorConfig.org
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# top-most EditorConfig file
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root = true
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[*]
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end_of_line = lf
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insert_final_newline = true
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charset = utf-8
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indent_style = space
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indent_size = 4
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[*.{yml,yaml}]
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indent_style = space
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indent_size = 2

‎.gitattributes‎

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*.smk linguist-language=Python
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Snakefile linguist-language=Python
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.test/* linguist-vendored=false
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.test/report.html linguist-generated=true

‎.github/workflows/main.yml‎

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name: Tests
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on:
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- push
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- pull_request
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jobs:
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run-workflow:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Checkout submodules
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uses: textbook/[email protected]
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- name: snakemake
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uses: snakemake/snakemake-github-action@master
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with:
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directory: .test
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snakefile: Snakefile
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args: "--use-conda --show-failed-logs"
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stagein: |
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conda create -c bioconda -c conda-forge -q -n prep bwa gatk4 samtools
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source activate prep
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bwa index .test/data/ref/genome.chr21.fa
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samtools faidx .test/data/ref/genome.chr21.fa
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gatk CreateSequenceDictionary -R .test/data/ref/genome.chr21.fa

‎.gitignore‎

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*
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!scripts
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!scripts/*
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!scripts/common
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!scripts/common/*
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scripts/.snakemake*
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!Snakefile
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!config.yaml
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!samples.tsv
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!resources
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!resources/*
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!envs
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!envs/*
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!environment.yaml
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!LICENSE
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!README.md
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!rules
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!rules/*
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!.gitignore
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!.gitattributes
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!.editorconfig
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!.travis.yml
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!.test
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!samples.tsv
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!units.tsv
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!schemas
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!schemas/*
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!.test/data
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!.test/samples.tsv
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!.test/units.tsv
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!.test/config.yaml
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!report
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!report/*.rst

‎.gitmodules‎

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[submodule ".test/data"]
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path = .test/data
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url = https://github.com/snakemake-workflows/ngs-test-data.git

‎.test/config.yaml‎

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samples: samples.tsv
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units: units.tsv
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ref:
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name: GRCh38.86
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genome: data/ref/genome.chr21.fa
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known-variants: data/ref/dbsnp.vcf.gz
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filtering:
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# Set to true in order to apply machine learning based recalibration of
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# quality scores instead of hard filtering.
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vqsr: false
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hard:
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# hard filtering as outlined in GATK docs
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# (https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set)
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snvs:
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"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"
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indels:
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"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"
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processing:
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remove-duplicates: true
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# restrict-regions: ../raw/captured_regions.bed
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# region-padding: 100
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params:
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gatk:
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HaplotypeCaller: ""
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BaseRecalibrator: ""
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GenotypeGVCFs: ""
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VariantRecalibrator: ""
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picard:
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MarkDuplicates: "REMOVE_DUPLICATES=true"
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trimmomatic:
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pe:
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trimmer:
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- "LEADING:3"
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- "TRAILING:3"
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- "SLIDINGWINDOW:4:15"
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- "MINLEN:36"
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se:
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trimmer:
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- "LEADING:3"
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- "TRAILING:3"
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- "SLIDINGWINDOW:4:15"
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- "MINLEN:36"

‎.test/report.html‎

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‎.test/samples.tsv‎

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sample
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A
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B

‎.test/units.tsv‎

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sample unit platform fq1 fq2
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A 1 ILLUMINA data/reads/a.chr21.1.fq data/reads/a.chr21.2.fq
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B 1 ILLUMINA data/reads/b.chr21.1.fq data/reads/b.chr21.2.fq
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B 2 ILLUMINA data/reads/b.chr21.1.fq

‎LICENSE‎

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MIT License
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Copyright (c) 2018, Johannes Köster
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

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