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Copy file name to clipboardExpand all lines: .dockstore.yml
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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description: "WDL workflow to align sequencing data using BWA and perform QC steps with GATK"
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topic: variant-calling
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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description: "WDL workflow to download raw sequencing data from ENA and align using STAR two-pass methodology"
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topic: rna-seq
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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description: "Convert paired FASTQ files to unmapped CRAM format using WILDS WDL modules"
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topic: alignment
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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- name: Louisa Goss
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email: lgoss2@fredhutch.org
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role: Research Associate
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0005-2936-2405
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orcid: 0009-0005-2936-2405
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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."
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topic: imputation
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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- name: Caroline Nondin
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email: cnondin@fredhutch.org
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role: Research Assistant
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0009-0955-5954
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orcid: 0009-0009-0955-5954
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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"
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topic: geospatial
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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- name: Sitapriya Moorthi
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email: smoorthi@fredhutch.org
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role: Staff Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0001-6372-5170
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orcid: 0000-0001-6372-5170
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description: "Consensus variant calling workflow for human panel/PCR-based targeted DNA sequencing with focus on leukemia analysis - Refactored with WILDS modules"
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topic: variant-calling
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Sitapriya Moorthi
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email: smoorthi@fredhutch.org
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role: Staff Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0001-6372-5170
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orcid: 0000-0001-6372-5170
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- name: Siobhan O'Brien
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email: sobrien2@fredhutch.org
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role: Post-Doctoral Research Fellow
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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description: "WDL workflow to download raw sequencing data from SRA and quantify using Salmon quasi-mapping"
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topic: rna-seq
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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description: "WDL workflow to download raw sequencing data from SRA and align using STAR two-pass methodology"
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topic: rna-seq
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filters:
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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- name: Emma Bishop
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email: ebishop@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0000-0003-4484-3336
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orcid: 0000-0003-4484-3336
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- name: Ethan Bouvet
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email: ebouvet@fredhutch.org
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role: Research Technician
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email: tfirman@fredhutch.org
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role: Research Informatics Data Scientist
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affiliation: Fred Hutch Cancer Center
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orcid: https://orcid.org/0009-0002-2052-1084
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orcid: 0009-0002-2052-1084
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description: "WDL pipeline for alternative splicing proteomics: STAR alignment, rMATS differential splicing detection, and JCAST protein sequence translation"
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