Explore Workflows

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

Graph Name Retrieved From View
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
workflow graph giab_haplotypecaller.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/giab_haplotypecaller.cwl

Branch/Commit ID: 0f8f97e6173085500b688ca8c601b1ce966dce33
workflow graph 02-trim-se.cwl

ATAC-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405
workflow graph AltAnalyze Prepare Genome

Devel version of AltAnalyze Prepare Genome ========================================== hg38 is not supported. Use hardcoded EnsMart72 until AltAnalyze starts support more recent Ensembl releases.

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

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
workflow graph 04-peakcall-se.cwl

ATAC-seq 04 quantification - SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl

Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 0b6e8fd8ead7644cf5398395b76af5cf4011686f
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 5c4125344b1b9125ad04d7e768ecc99901570a7a
workflow graph kfdrc_process_bam.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: subworkflows/kfdrc_process_bam.cwl

Branch/Commit ID: 105340db0e99918fd7e8a8e14f1cde3022b44653