Workflow Type: Galaxy

COVID-19: variation analysis reporting

This workflow takes VCF datasets of variants produced by any of the variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular reports of variants by samples and by variant, along with an overview plot of variants and their allele-frequencies across all samples.

Inputs

ID Name Description Type
AF Filter AF Filter Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports. n/a
DP Filter DP Filter Depth Filter. This is the minimum depth of all alignments at a variant site. n/a
Variation data to report Variation data to report Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling n/a
DP_ALT Filter DP_ALT Filter Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant. n/a
gene products translations gene products translations A custom tabular file mapping NCBI RefSeq Protein identifiers as used by snpEff version 4.5covid19 to their commonly used names. Can be obtained from https://doi.org/10.5281/zenodo.4555734 n/a
Number of Clusters Number of Clusters Number of Clusters to use in Variant Frequency Plot. n/a
in_file in_file runtime parameter for tool Datamash n/a

Steps

ID Name Description
0 AF Filter Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.
1 DP Filter Depth Filter. This is the minimum depth of all alignments at a variant site.
2 Variation data to report Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling
3 DP_ALT Filter Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.
4 gene products translations A custom tabular file mapping NCBI RefSeq Protein identifiers as used by snpEff version 4.5covid19 to their commonly used names. Can be obtained from https://doi.org/10.5281/zenodo.4555734
5 Number of Clusters Number of Clusters to use in Variant Frequency Plot.
6 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
7 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
8 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
10 SnpSift Extract Fields toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
11 Replace column toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2
12 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
13 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
14 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
15 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
16 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
17 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
18 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
19 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
20 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
21 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
22 Filter Filter1
23 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
24 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
25 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
26 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
27 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
28 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
29 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
30 Cut Cut1
31 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
32 Cut Cut1
33 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
34 Cut Cut1
35 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
36 Variant Frequency Plot toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3
37 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
38 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1

Outputs

ID Name Description Type
output output n/a
out1 out1 n/a
out1 out1 n/a
output output n/a
output output n/a
outfile_replace outfile_replace n/a
out_file1 out_file1 n/a
out_file out_file n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
output output n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
outfile outfile n/a
out_file out_file n/a
out_file1 out_file1 n/a
out_file out_file n/a
output output n/a
out_file out_file n/a
out_file out_file n/a
out_file out_file n/a
output output n/a
output output n/a
out_file1 out_file1 n/a
output output n/a
out_file1 out_file1 n/a
outfile outfile n/a
out_file1 out_file1 n/a
list_output_tab list_output_tab n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a

Version History

v0.2 (latest) Created 18th Feb 2022 at 03:00 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 c837d94

v0.1.3 Created 5th Feb 2022 at 03:00 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 a964e92

v0.1.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Open master 6448ba3

v0.1.1 Created 27th Jul 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen master d75c2bc

v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot

Added/updated 13 files


Frozen master 7ce82db
help Creators and Submitter
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Additional credit

Wolfgang Maier

Submitter
License
Activity

Views: 1877

Created: 12th Mar 2021 at 13:41

Last updated: 18th Feb 2022 at 03:00

Last used: 28th Jun 2022 at 08:18

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Total size: 252 KB
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