Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf_clipseqcore_pe_2barcodes.cwl

Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs

https://github.com/YeoLab/eclip.git

Path: cwl/wf_clipseqcore_pe_2barcodes.cwl

Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0
workflow graph wf_trim_and_map_se.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_se.cwl

Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 700e73aaed6db1ad538dd27b2e1709f436ad3edb
workflow graph Dockstore.cwl

https://github.com/wshands/ghapps-single-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: fe907a47040554f3e77694e02313321b0f64f265
workflow graph Filter Protein Alignments I

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 742dbafb5fb103d8578f48a0576c14dd8dae3b2a
workflow graph wf_clipseqcore_pe_1barcode.cwl

Workflow for handling reads containing one barcode. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs

https://github.com/YeoLab/eclip.git

Path: cwl/wf_clipseqcore_pe_1barcode.cwl

Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec
workflow graph wf_trim_and_map_pe.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_pe.cwl

Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0