Workflow Type: Galaxy
Open
Frozen
From Fastqs to VCFs and BAMs
Associated Tutorial
This workflows is part of the tutorial From Fastqs to VCFs and BAMs, available in the GTN
Thanks to...
Tutorial Author(s): Galo A. Goig, Daniela Brites, Christoph Stritt
Tutorial Contributor(s): Wolfgang Maier
Inputs
ID | Name | Description | Type |
---|---|---|---|
Mycobacterium_tuberculosis_ancestral_reference.gbk | #main/Mycobacterium_tuberculosis_ancestral_reference.gbk | n/a |
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Paired-End FASTQs | #main/Paired-End FASTQs | n/a |
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Single-End FASTQs | #main/Single-End FASTQs | n/a |
|
Steps
ID | Name | Description |
---|---|---|
3 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
4 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
5 | Mapping and variant calling of SINGLE END FASTQs with snippy | toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 |
6 | Mapping and variant calling of PAIRED END FASTQs with snippy | toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 |
7 | Merge PE/SE VCFs in a single collection with all samples | __MERGE_COLLECTION__ |
8 | Merge PE/SE BAMs in a single collection with all samples (Part the workflow "Identifying DR with TB-profiler) | __MERGE_COLLECTION__ |
9 | TB Variant Filter | toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
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_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:24 by Helena Rasche
Added/updated 4 files
Open
master
9c6125d
2.0 (earliest) Created 25th Jun 2024 at 11:22 by Helena Rasche
Added/updated 4 files
Frozen
2.0
2018e83
Creators and Submitter
Creators
Not specifiedSubmitter
Discussion Channel
Activity
Views: 451 Downloads: 129
Created: 25th Jun 2024 at 11:22
Last updated: 25th Jun 2024 at 11:22
Attributions
None