Explore Workflows

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

Path: tests/inp_update_wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 9144d08fa7f4e852498761481dceab477167fa65

The first step of the workflow consists of converting the raw mass spectrometry data to the mzML format using msconvert, followed by the database search using MSFragger, and the peptide validation using PeptideProphet. #End-user license agreement (EULA) A central tool in this workflow is MSFragger which can only be used for academic research, non-commercial or educational purposes. To run this workflow you must accept the EULA below. ``` #7143 - MSFragger - Academic and Research Education Use License This license includes a digital file, available for download after the license agreement has been executed and approved (if necessary) which includes the University of Michigan PROGRAM. NOTICE: MSFragger utilizes the MSFTBX library to read mzXML and mzML files. The MSFTBX uses third-party software that is subject to open source and/or third-party license terms. These terms are attached in the file LICENSE-3RD-PARTY.txt. By accepting the terms and conditions of this Agreement, LICENSEE will also be subject to those terms and conditions. PROGRAM: MSFragger UM # 7143 - Philosopher Pipeline Distribution Permissions - Cancer Genomics Cloud This Agreement is made by and between The Regents of The University of Michigan, a constitutional corporation of the state of Michigan (hereinafter \"MICHIGAN\") and LICENSEE. BACKGROUND 1. Members of the University of Michigan’s Medical School Departments of Pathology and Computational Medicine and Bioinformatics have developed a proprietary software application and related documentation for peptide identification referred to as “MSFragger”, for use by trained individuals in bioinformatics and proteomics research (hereinafter referred to as \"PROGRAM\"); and 2. LICENSEE desires to obtain, and MICHIGAN, consistent with its mission of education and research, desires to grant, a license to use the PROGRAM subject to the terms and conditions set forth below; and The parties therefore agree as follows: I. LICENSE MICHIGAN hereby grants to LICENSEE a non-exclusive, non-transferable right to use the PROGRAM solely for academic research, non-commercial or educational purposes within the LICENSEE’s department and subject to the terms and conditions of this Agreement. Commercial use of any kind of the PROGRAM is strictly prohibited. This license is solely for deployment of the PROGRAM in conjunction with the Cancer Genomics Cloud project. No other license rights are granted. II. LIMITATION OF LICENSE AND RESTRICTIONS A. LICENSEE shall not use, print, copy, translate, reverse engineer, decompile, disassemble, modify, create derivative works of or publicly display the PROGRAM, in whole or in part, unless expressly authorized by this Agreement. B. LICENSEE agrees that it shall use the PROGRAM only for LICENSEE'S sole and exclusive use, and shall not disclose, sell, license, or otherwise distribute the PROGRAM, in whole or in part, to any third party without the prior written consent of MICHIGAN. LICENSEE shall not assign this Agreement, and any attempt by LICENSEE to assign it shall be void from the beginning. LICENSEE agrees to secure and protect the PROGRAM and any copies of the PROGRAM in a manner consistent with the maintenance of MICHIGAN'S rights in the PROGRAM and to take appropriate action by instruction or agreement with its employees who are permitted access to the PROGRAM in order to satisfy LICENSEE'S obligations under this Agreement. C. LICENSEE may copy the PROGRAM for the purpose of using the PROGRAM on other devices and for archival purposes. D. Such license shall be only for its intended use and in accordance with applicable Food and Drug Administration (FDA) regulations for pre-clinical and clinical research, including, but not limited to, applicable investigational device exemption (IDE) regulations, institutional review board (IRB) approval, required protocols and monitoring of the study, required records and reports, and applicable protection of human subjects regulations. E. LICENSEE agrees to acknowledge MICHIGAN in scientific publications resulting (in part) of the use of the PROGRAM, by making reference to the publication of the PROGRAM when it becomes available in the scientific literature. Copyright notice should be as follows, “MSFragger © 2016 The Regents of the University of Michigan.” III. CONSIDERATION A no-cost option for the license rights granted in this Agreement. IV. TITLE AND OWNERSHIP A. No ownership rights of MICHIGAN in the PROGRAM are conferred upon LICENSEE by this Agreement. B. LICENSEE acknowledges MICHIGAN'S proprietary rights in the PROGRAM and agrees to reproduce all copyright notices supplied by MICHIGAN on all copies of the PROGRAM. C. LICENSEE agrees this license is explicitly for academic research applications only and that it cannot be used for commercial purposes of any kind. LICENSEE further acknowledges that any use in a commercial setting will be subject to prosecution to the fullest extent available under the law and remedies may include full recovery of legal, operational, economic and other losses which the LICENSEE will be directly liable for. V. DISCLAIMER OF WARRANTY AND LIMITATION OF LIABILITY A. THE PROGRAM IS PROVIDED \"AS IS\" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. MICHIGAN DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN THE PROGRAM WILL MEET LICENSEE'S REQUIREMENTS OR THAT OPERATION WILL BE UNINTERRUPTED OR ERROR FREE. MICHIGAN shall not be liable for special, indirect, incidental, or consequential damages with respect to any claim on account of or arising from this Agreement or use of the PROGRAM, even if MICHIGAN has been or is hereafter advised of the possibility of such damages. Because some states do not allow certain exclusions or limitations on implied warranties or of liability for consequential or incidental damages, the above exclusions may not apply to LICENSEE. In no event, however, will MICHIGAN be liable to LICENSEE, under any theory of recovery, in an amount in excess of the license fee paid by LICENSEE under this Agreement. B. LICENSEE agrees that MICHIGAN has no obligation to provide to LICENSEE any maintenance, support, or update services. Should MICHIGAN provide any revised versions of the PROGRAM to LICENSEE, LICENSEE agrees that this license agreement shall apply to such revised versions. VI. WARRANTY OF LICENSEE LICENSEE warrants and represents that it will carefully review any documentation or instructional material provided by MICHIGAN. VIII. TERMINATION If LICENSEE at any time fails to abide by the terms of this Agreement, MICHIGAN shall have the right to immediately terminate the license granted herein, require the return or destruction of all copies of the PROGRAM from LICENSEE and certification in writing as to such return or destruction, and pursue any other legal or equitable remedies available. VIII. MISCELLANEOUS A. This Agreement shall be construed in accordance with the laws of the state of Michigan. Should LICENSEE for any reason bring a claim, demand, or other action against MICHIGAN, its agents or employees, arising out of this Agreement or the PROGRAM licensed herein, LICENSEE agrees to bring said claim only in the Michigan Court of Claims. B. THIS AGREEMENT REPRESENTS THE COMPLETE AND EXCLUSIVE STATEMENT OF THE AGREEMENT BETWEEN MICHIGAN AND LICENSEE AND SUPERSEDES ALL PRIOR AGREEMENTS, PROPOSALS, REPRESENTATIONS AND OTHER COMMUNICATIONS, VERBAL OR WRITTEN, BETWEEN THEM WITH RESPECT TO USE OF THE PROGRAM. THIS AGREEMENT MAY BE MODIFIED ONLY WITH THE MUTUAL WRITTEN APPROVAL OF AUTHORIZED REPRESENTATIVES OF THE PARTIES. C. The terms and conditions of this Agreement shall prevail notwithstanding any different, conflicting, or additional terms or conditions which may appear in any purchase order or other document submitted by LICENSEE. LICENSEE agrees that such additional or inconsistent terms are deemed rejected by MICHIGAN. D. Unless otherwise exempt therefrom, LICENSEE agrees that it will be responsible for any sales, use or excise taxes imposed by any governmental unit in this transaction except income taxes. E. LICENSEE acknowledges that the PROGRAM is of United States origin. LICENSEE agrees to comply with all applicable international and national laws that apply to the PROGRAM, including the United States Export Administration Regulations, as well as end-user, end-use, and destination restrictions issued by the United States. F. MICHIGAN and LICENSEE agree that any xerographically or electronically reproduced copy of this fully-executed agreement shall have the same legal force and effect as any copy bearing original signatures of the parties. G. MSFragger utilizes the MSFTBX library to read mzXML and mzML files. The MSFTBX uses third-party software that is subject to open source and/or third-party license terms. These terms are attached in the file LICENSE-3RD-PARTY.txt. By accepting the terms and conditions of this Agreement, LICENSEE will also be subject to those terms and conditions ```

https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial.git

Path: FragPipe-Convert-Identify-PeptideProphet/fragpipe-convert-identify-peptideprophet.cwl

Branch/Commit ID: 080063b7443c98bc378935e16f747f8c542c9521

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_create_readme/readme-genePrediction-workflow.cwl

Branch/Commit ID: b1e1b906fcfb2c0fad8811fb8ab03009282c1d19

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86

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

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3

Motif Finding with HOMER with random background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis.cwl

Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/transform.cwl

Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e

https://github.com/ryanratcliff/docker_java8.git

Path: word-count-aggregator.cwl

Branch/Commit ID: 003030fc7540bc5ecd64a8f6e85ba86218764ca6