COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Changelog

[0.1.5] 2024-03-05

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
• toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 was updated to toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 was updated to toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
• toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2

[0.1.4] 2023-11-20

• Fix author in dockstore
• Fix input fastq URL for test
• Update output test

[0.1.3] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.1.2] 2021-07-23

Added

Added RO-Crate metadata file. No functional changes.

[0.1.1] 2021-06-14

Fixed

Fix reference to test file in .dockstore.yml

[0.1]

• Initial version of COVID-19: variation analysis on WGS SE data workflow

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
• toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
• toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2
• toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19