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Merge pull request #32 from MPUSP/improvements
feat!: refactoring of workflow to make it more flexible, remove hardcoded options
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‎.editorconfig‎

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‎.github/workflows/conventional-prs.yml‎

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name: Lint PR
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name: Conventional PRs
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on:
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pull_request_target:
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types:
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pull-requests: read
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jobs:
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main:
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name: Validate PR title
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runs-on: ubuntu-latest
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steps:
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- uses: amannn/action-semantic-pull-request@v5
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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conventional-prs:
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uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main

‎.github/workflows/deploy-apptainer.yml‎

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name: Deploy Apptainer
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on:
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workflow_run:
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workflows: ["Release Please"]
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types:
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- completed
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workflow_dispatch:
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permissions:
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contents: read
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packages: write
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jobs:
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deploy-apptainer:
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if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
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uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main

‎.github/workflows/main.yml‎

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‎.github/workflows/release-please.yml‎

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name: Release Please
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on:
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push:
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branches:
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- main
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branches: [main]
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permissions:
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contents: write
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pull-requests: write
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name: release-please
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issues: write
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jobs:
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release-please:
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runs-on: ubuntu-latest
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steps:
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- uses: googleapis/release-please-action@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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release-type: simple
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uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main

‎.github/workflows/snakemake-tests.yml‎

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name: Snakemake Tests
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on:
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pull_request:
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branches: [main]
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jobs:
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snakemake-tests:
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uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
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with:
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cores: 2
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dryrun: false

‎.snakemake-workflow-catalog.yml‎

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# configuration of display in snakemake workflow catalog: https://snakemake.github.io/snakemake-workflow-catalog
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usage:
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software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
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conda: true # whether pipeline works with --use-conda
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singularity: false # whether pipeline works with --use-singularity
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singularity+conda: false # whether pipeline works with --use-singularity --use-conda
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report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
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mandatory-flags:
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desc: # describe your flags here in a few sentences
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flags: # put your flags here
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software-stack-deployment:
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conda: true # whether pipeline works with '--sdm conda'
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apptainer: false # whether pipeline works with '--sdm apptainer/singularity'
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apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
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report: true # whether creation of reports using 'snakemake --report report.zip' is supported

‎.test/config/config.yml‎

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samplesheet: "config/samplesheet/samples_mpusp_custom.tsv"
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libtype: "sense"
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samplesheet: "config/samplesheet/samples_neb_umi.tsv"
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libtype: "antisense"
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get_genome:
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database: "ncbi"
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"RefSeq": "gene",
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"RefSeq": "pseudogene",
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"RefSeq": "CDS",
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"Protein Homology": "CDS"
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"Protein Homology": "CDS",
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]
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extract_features:
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biotypes: ["protein_coding", "pseudogene", "ncRNA", "rRNA", "tRNA"]
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umi_extraction:
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method: "string"
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pattern: "--bc-pattern=NNNCCCNNNCCCNNNC"
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method: "none"
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pattern: ""
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umi_dedup: "--edit-distance-threshold=0"
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cutadapt:
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read1_adapter: "TACACGACGCTCTTCCGATCT"
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read2_adapter: "AGATCGGAAGAGCGTCGTGTA"
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default:
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[
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"-q 10 ",
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"-m 18 ",
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"--overlap=3"
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]
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fastp:
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extra: "-M 10 -l 18 --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
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star:
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index: Null
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genomeSAindexNbases: 9
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multi: 10
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sam_multi: 1
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intron_max: 1
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default:
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index: "--genomeSAindexNbases 9"
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extra:
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[
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"--readFilesCommand zcat ",
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"--outSAMstrandField None ",
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"--outSAMattributes All ",
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"--outSAMattrIHstart 0 ",
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"--outFilterType Normal ",
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"--outFilterMultimapScoreRange 1 ",
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"-o STARmappings ",
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"--outSAMtype BAM Unsorted ",
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"--outStd BAM_Unsorted ",
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"--outMultimapperOrder Random ",
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"--alignEndsType EndToEnd",
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"--outFilterMultimapNmax 10",
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"--outSAMmultNmax 1",
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"--outMultimapperOrder Random",
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"--alignIntronMax 1",
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]
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samtools:
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sort: ""
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index: ""
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feature_counts:
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defaults:
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[
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"-g locus_tag",
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"-M",
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"--fracOverlap 0.2",
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"--largestOverlap"
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"--largestOverlap",
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]
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deeptools:
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bin_size: 1
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normalize: "CPM"
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defaults: "--exactScaling"
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paired_end: "--extendReads"
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genome_size: 2000000
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extra: "--binSize 1 --normalizeUsing CPM --exactScaling --extendReads"
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fastqc:
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extra: "--quiet --nogroup"
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multiqc:
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config: "config/multiqc_config.yml"
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defaults: ["--dirs-depth 2 ",
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"--exclude general_stats ",
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"--force ",
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"--dirs"]
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config: "config/multiqc_config.yml"
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extra: "--dirs"

‎.test/config/multiqc_config.yml‎

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report_header_info:
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- Snakemake workflow: https://github.com/MPUSP/snakemake-bacterial-rnaseq-processing
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- Contact E-mail: "bioinformatics@mpusp.mpg.de"
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- Application Type: "Bacterial RNAseq"
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- Sequencing Platform: "Illumina"
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custom_logo_title: "Max Planck Unit for the Science of Pathogens"
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skip_versions_section: false
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disable_version_detection: true
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disable_version_detection: false
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versions_table_group_header: "Workflow Analysis Steps"
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skip_generalstats: true
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- samtools-stats
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module_order:
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- fastqc
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- fastp
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- star
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- cutadapt
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- fastqc:
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name: "FastQC (trimmed)"
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anchor: "fastqc_trimmed"
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info: "This section of the report shows FastQC results after adapter trimming."
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target: ""
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path_filters:
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- "*/clipped_reads/*_fastqc.zip"
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- fastqc:
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name: "FastQC (raw)"
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anchor: "fastqc_raw"
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path_filters:
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- "*/raw_reads/*_fastqc.zip"
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report_section_order:
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fastqc_raw:
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before: fastqc_trimmed
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- umitools
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- featurecounts
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- samtools
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- biotype_dist

‎.test/config/samplesheet/samples_mpusp_custom.tsv‎

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sample condition replicate experiment data_folder fq1 fq2 fq_umi
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RNA-1 RNA 1 rnaseq_mpusp_custom data/rnaseq_mpusp_custom RNA-1_R1.fastq.gz RNA-1_R2.fastq.gz -
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RNA-2 RNA 2 rnaseq_mpusp_custom data/rnaseq_mpusp_custom RNA-2_R1.fastq.gz RNA-2_R2.fastq.gz -
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sample condition replicate read1 read2 readumi
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RNA-1 RNA 1 data/rnaseq_mpusp_custom/RNA-1_R1.fastq.gz data/rnaseq_mpusp_custom/RNA-1_R2.fastq.gz -
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RNA-2 RNA 2 data/rnaseq_mpusp_custom/RNA-2_R1.fastq.gz data/rnaseq_mpusp_custom/RNA-2_R2.fastq.gz -

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