Workflow Type: Galaxy
Open
Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh
Inputs
ID | Name | Description | Type |
---|---|---|---|
Forwards reads | Forwards reads | n/a |
|
Reverse reads | Reverse reads | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | Trim Galore! | toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 |
3 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
4 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
5 | Filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_3 | _anonymous_output_3 | n/a |
|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
Version History
Version 1 (earliest) Created 2nd Feb 2021 at 19:06 by ignacio eguinoa
Added/updated 1 files
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master
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Created: 2nd Feb 2021 at 19:06
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