From Fastqs to VCFs and BAMs

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Workflow Type: Galaxy

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1305?version=2

Inputs

ID Name Description Type
Mycobacterium_tuberculosis_ancestral_reference.gbk #main/Mycobacterium_tuberculosis_ancestral_reference.gbk n/a
  • File
Paired-End FASTQs #main/Paired-End FASTQs n/a
  • array containing
    • File
Single-End FASTQs #main/Single-End FASTQs n/a
  • array containing
    • File

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
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

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
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
Trimmomatic
snippy
COMBAT-TB Workbench
License
Creative Commons Attribution 4.0 International
Activity

Views: 460   Downloads: 135

Created: 25th Jun 2024 at 11:22

Last updated: 25th Jun 2024 at 11:22

help Attributions

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Total size: 80.7 KB
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