Explore Workflows

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

Graph Name Retrieved From View
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: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31
workflow graph tmb.cwl

Workflow for calculating TMB tumor mutational burden on a single sample

https://github.com/mskcc/pluto-cwl.git

Path: cwl/tmb.cwl

Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e
workflow graph genomics-workspace-genome.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945
workflow graph workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_md5checksums/workflow.cwl

Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729
workflow graph WGS QC workflow nonhuman

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

Path: definitions/subworkflows/qc_wgs_nonhuman.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620
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: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256
workflow graph tmb.cwl

Workflow for calculating TMB tumor mutational burden on a single sample

https://github.com/mskcc/pluto-cwl.git

Path: cwl/tmb.cwl

Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4
workflow graph fail-unconnected.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/fail-unconnected.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050