Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/cle_somatic_exome.cwl

Branch/Commit ID: bcc6adaf15035f5ce6fc851e27b1173b0fd20c1c
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 25aa4788dd4efb1cc8ed6f609cb7803896e4d28d
workflow graph sec-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/umi_molecular_alignment.cwl

Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157
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: 3fc68366adb179927af5528c27b153abaf94494d
workflow graph any-type-compat.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph Nested workflow example

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/nested.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

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

Path: workflows/bwa-index.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3