Workflow Type: Galaxy

COVID-19: variation analysis reporting

This workflow takes table of variants produced by any of the other four variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates a list of variants by Samples and by Variant.

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 report. 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://zenodo.org/record/4555735 n/a
Number of Clusters Number of Clusters Number of Clusters to find in Variant Frequency Plot. 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 report.
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://zenodo.org/record/4555735
5 Number of Clusters Number of Clusters to find in Variant Frequency Plot.
6 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
7 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
8 SnpSift Filter toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
9 SnpSift Extract Fields toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
10 Replace column toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2
11 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
12 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
13 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
14 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
15 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.5
16 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.5
17 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
18 Filter Filter1
19 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
20 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
21 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
22 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
23 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
24 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
25 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
26 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
27 Cut Cut1
28 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
29 Cut Cut1
30 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
31 Cut Cut1
32 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
33 Variant Frequency Plot toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3
34 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
35 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1

Outputs

ID Name Description Type
out1 out1 n/a
out1 out1 n/a
output output n/a
output output n/a
outfile_replace outfile_replace n/a
out_file out_file 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_file1 out_file1 n/a
out_file out_file 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
output output n/a
out_file out_file n/a
out_file1 out_file1 n/a
output output n/a
out_file1 out_file1 n/a
list_output_tab list_output_tab n/a
out_file1 out_file1 n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
outfile outfile n/a
help Creators and Submitter
Creator
  • Wolfgang Maier
Submitter
License
Activity

Views: 145   Downloads: 1

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

Last used: 25th Oct 2021 at 20:54

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Version History

Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo

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Version 2 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

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