version: 1.2

workflows:
  # =============================================================================
  # PIPELINES - Complete analysis workflows combining multiple modules
  # =============================================================================

  - name: ww-bwa-gatk
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-bwa-gatk/ww-bwa-gatk.wdl
    readMePath: /pipelines/ww-bwa-gatk/README.md
    testParameterFiles:
      - /pipelines/ww-bwa-gatk/inputs.json
    authors:
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
    description: "WDL workflow to align sequencing data using BWA and perform QC steps with GATK"
    topic: variant-calling
    filters:
      branches:
        - main
      tags:
        - genomics
        - alignment
        - variant-calling
        - bwa
        - gatk

  - name: ww-ena-star
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-ena-star/ww-ena-star.wdl
    readMePath: /pipelines/ww-ena-star/README.md
    testParameterFiles:
      - /pipelines/ww-ena-star/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
    description: "WDL workflow to download raw sequencing data from ENA and align using STAR two-pass methodology"
    topic: rna-seq
    filters:
      branches:
        - main
      tags:
        - genomics
        - rna-seq
        - alignment
        - star
        - ena

  - name: ww-fastq-to-cram
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-fastq-to-cram/ww-fastq-to-cram.wdl
    readMePath: /pipelines/ww-fastq-to-cram/README.md
    testParameterFiles:
      - /pipelines/ww-fastq-to-cram/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
    description: "Convert paired FASTQ files to unmapped CRAM format using WILDS WDL modules"
    topic: alignment
    filters:
      branches:
        - main
      tags:
        - genomics
        - format-conversion
        - fastq
        - cram
        - samtools

  - name: ww-imputation
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-imputation/ww-imputation.wdl
    readMePath: /pipelines/ww-imputation/README.md
    testParameterFiles:
      - /pipelines/ww-imputation/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
      - name: Louisa Goss
        email: lgoss2@fredhutch.org
        role: Research Associate
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0005-2936-2405
    description: "WDL workflow for genotype imputation from low-coverage WGS data using GLIMPSE2. Processes CRAM/BAM files against a reference panel to produce imputed VCF files."
    topic: imputation
    filters:
      branches:
        - main
      tags:
        - genomics
        - imputation
        - glimpse2
        - low-coverage-wgs
        - genotyping

  - name: ww-jetlag
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-jetlag/ww-jetlag.wdl
    readMePath: /pipelines/ww-jetlag/README.md
    testParameterFiles:
      - /pipelines/ww-jetlag/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
      - name: Caroline Nondin
        email: cnondin@fredhutch.org
        role: Research Assistant
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0009-0955-5954
    description: "WDL pipeline to calculate sunrise/sunset times and sun time differences across an array of geographic tiles as part of the SJL model pipeline"
    topic: geospatial
    filters:
      branches:
        - main
      tags:
        - geospatial
        - solar-jetlag
        - environmental-health
        - sunrise-sunset

  - name: ww-leukemia
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-leukemia/ww-leukemia.wdl
    readMePath: /pipelines/ww-leukemia/README.md
    testParameterFiles:
      - /pipelines/ww-leukemia/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
      - name: Sitapriya Moorthi
        email: smoorthi@fredhutch.org
        role: Staff Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0001-6372-5170
    description: "Consensus variant calling workflow for human panel/PCR-based targeted DNA sequencing with focus on leukemia analysis - Refactored with WILDS modules"
    topic: variant-calling
    filters:
      branches:
        - main
      tags:
        - genomics
        - variant-calling
        - leukemia
        - targeted-sequencing
        - consensus-calling

  - name: ww-saturation
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-saturation/ww-saturation.wdl
    readMePath: /pipelines/ww-saturation/README.md
    testParameterFiles:
      - /pipelines/ww-saturation/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Sitapriya Moorthi
        email: smoorthi@fredhutch.org
        role: Staff Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0001-6372-5170
      - name: Siobhan O'Brien
        email: sobrien2@fredhutch.org
        role: Post-Doctoral Research Fellow
        affiliation: Fred Hutch Cancer Center
    description: "WDL workflow to analyze saturation mutagenesis data using BWA alignment and GATK AnalyzeSaturationMutagenesis"
    topic: saturation-mutagenesis
    filters:
      branches:
        - main
      tags:
        - genomics
        - saturation-mutagenesis
        - bwa
        - gatk
        - functional-genomics

  - name: ww-sra-salmon
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-sra-salmon/ww-sra-salmon.wdl
    readMePath: /pipelines/ww-sra-salmon/README.md
    testParameterFiles:
      - /pipelines/ww-sra-salmon/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
    description: "WDL workflow to download raw sequencing data from SRA and quantify using Salmon quasi-mapping"
    topic: rna-seq
    filters:
      branches:
        - main
      tags:
        - genomics
        - rna-seq
        - quantification
        - salmon
        - sra

  - name: ww-sra-star
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-sra-star/ww-sra-star.wdl
    readMePath: /pipelines/ww-sra-star/README.md
    testParameterFiles:
      - /pipelines/ww-sra-star/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
    description: "WDL workflow to download raw sequencing data from SRA and align using STAR two-pass methodology"
    topic: rna-seq
    filters:
      branches:
        - main
      tags:
        - genomics
        - rna-seq
        - alignment
        - star
        - sra

  - name: ww-star-deseq2
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-star-deseq2/ww-star-deseq2.wdl
    readMePath: /pipelines/ww-star-deseq2/README.md
    testParameterFiles:
      - /pipelines/ww-star-deseq2/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
      - name: Emma Bishop
        email: ebishop@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0000-0003-4484-3336
      - name: Ethan Bouvet
        email: ebouvet@fredhutch.org
        role: Research Technician
        affiliation: Fred Hutch Cancer Center
    description: "WDL workflow for RNA-seq alignment via STAR and DESeq2 differential expression analysis"
    topic: differential-expression
    filters:
      branches:
        - main
      tags:
        - genomics
        - rna-seq
        - differential-expression
        - star
        - deseq2

  - name: ww-splicing-proteomics
    subclass: WDL
    primaryDescriptorPath: /pipelines/ww-splicing-proteomics/ww-splicing-proteomics.wdl
    readMePath: /pipelines/ww-splicing-proteomics/README.md
    testParameterFiles:
      - /pipelines/ww-splicing-proteomics/inputs.json
    authors:
      - name: Taylor Firman
        email: tfirman@fredhutch.org
        role: Research Informatics Data Scientist
        affiliation: Fred Hutch Cancer Center
        orcid: 0009-0002-2052-1084
    description: "WDL pipeline for alternative splicing proteomics: STAR alignment, rMATS differential splicing detection, and JCAST protein sequence translation"
    topic: proteogenomics
    filters:
      branches:
        - main
      tags:
        - genomics
        - proteogenomics
        - alternative-splicing
        - rmats
        - jcast
        - star