Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Preprocess fastq

Remove and trim low quality reads from fastq files. Return fasta files with reads passed and reads removed.

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/preprocess-fastq.workflow.cwl

Branch/Commit ID: 721aaf285e1848c3c52da38a1fed95192aeff8f4
workflow graph abundance

abundace profiles from annotated files, for protein and/or rna

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/abundance.workflow.cwl

Branch/Commit ID: 721aaf285e1848c3c52da38a1fed95192aeff8f4
workflow graph Tumor-Only Detect Variants workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec
workflow graph Replace legacy AML Trio Assay

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

 https://github.com/datirium/workflows.git

Path: workflows/rgt-thor.cwl

Branch/Commit ID: ee66d03be8a7fd61367db40c37a973ff55ece4da
workflow graph umi duplex alignment workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: f77a920bcc73f6cfdb091eed75a149d02cd8a263
workflow graph AltAnalyze Build Reference Indices

AltAnalyze Build Reference Indices ==================================

 https://github.com/datirium/workflows.git

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca
workflow graph kmer_cache_store

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: ae781871782805632f8947c1b11f65507c80cd43
workflow graph Whole genome alignment and somatic variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/somatic_wgs.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph scatter GATK HaplotypeCaller over intervals

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c