Explore Workflows

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

Graph Name Retrieved From View
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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

Path: workflows/feature-merge.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph scatter-valuefrom-wf6.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c
workflow graph conflict-wf.cwl#collision

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c

Packed ID: collision
workflow graph genome-kallisto-index.cwl

Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index

https://github.com/Barski-lab/workflows.git

Path: tools/genome-kallisto-index.cwl

Branch/Commit ID: 80d64741638b14de5cf58236b6d6d99713c62086
workflow graph stdout-wf_v1_0.cwl

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

Path: testdata/stdout-wf_v1_0.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127
workflow graph grepsort workflow

a workflow that performs grep followed by sort

 https://github.com/ResearchObject/runcrate.git

Path: tests/data/grepsort-run-1/snapshot/grepsort.cwl

Branch/Commit ID: 376f6b2c6332a4742d4512d6e1fb785a2f8b7285
workflow graph count-lines10-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph kfdrc_alignment_pipeline.cwl

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

Path: dev/pilot-run/worklflows/kfdrc_alignment_pipeline.cwl

Branch/Commit ID: 4b8dc1e00d3dd082ee31629afdeda6103f75dc3a
workflow graph fasta2taxa-plot

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

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

Path: CWL/Workflows/qiime/join-reads2plot.cwl

Branch/Commit ID: b8c2be41cd8805023a0d9e5916042b2557205d03
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: 261c0232a7a40880f2480b811ed2d7e89c463869