Trio Analysis Version 1
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Run on usegalaxy.eu
Workflow Type: Galaxy
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| pedigree | pedigree | n/a | n/a |
| input | input | runtime parameter for tool Filter | n/a |
| sec_header | sec_header | runtime parameter for tool bcftools merge | n/a |
| intervals | intervals | runtime parameter for tool SnpEff eff: | n/a |
| transcripts | transcripts | runtime parameter for tool SnpEff eff: | n/a |
Steps
| ID | Name | Description |
|---|---|---|
| 0 | EGA Download Client | toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/4.0.0+galaxy0 |
| 1 | EGA Download Client | toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/4.0.0+galaxy0 |
| 2 | pedigree | |
| 3 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 4 | EGA Download Client | toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/4.0.0+galaxy0 |
| 5 | Convert compressed file to uncompressed. | CONVERTER_gz_to_uncompressed |
| 6 | Column Regex Find And Replace | Add chr prefix toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 |
| 7 | bcftools norm | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1 |
| 8 | Filter | Filter1 |
| 9 | bcftools merge | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10 |
| 10 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
| 11 | GEMINI load | toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 |
| 12 | GEMINI inheritance pattern | toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| authorized_datasets | authorized_datasets | n/a | |
| dataset_file_list | dataset_file_list | n/a | |
| output | output | n/a | |
| downloaded_file_collection | downloaded_file_collection | n/a | |
| output1 | output1 | n/a | |
| out_file1 | out_file1 | n/a | |
| output_file | output_file | n/a | |
| out_file1 | out_file1 | n/a | |
| output_file | output_file | n/a | |
| snpeff_output | snpeff_output | n/a | |
| statsFile | statsFile | n/a | |
| outfile | outfile | n/a | |
| outfile | outfile | n/a |
Version History
Version 1 (earliest) Created 9th Jun 2022 at 09:32 by Helena Rasche
Initial commit
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masterc2cc6af
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Views: 119
Created: 9th Jun 2022 at 09:32
Last used: 28th Jun 2022 at 22:09
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Organizations: Not specified
https://orcid.org/0000-0001-9760-8992
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
Space: This Team is not associated with a Space
Public web page: https://training.galaxyproject.org
Start date: 1st Sep 2017
