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.
  • float?
DP Filter DP Filter Depth Filter. This is the minimum depth of all alignments at a variant site.
  • int?
DP_ALT Filter DP_ALT Filter Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.
  • int?
Number of Clusters Number of Clusters Number of Clusters to find in Variant Frequency Plot.
  • int?
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
  • File[]
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
  • File

Steps

ID Name Description
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
filtered_variants filtered_variants n/a
  • File
filtered_extracted_variants filtered_extracted_variants n/a
  • File
filtered_and_renamed_effects filtered_and_renamed_effects n/a
  • File
collapsed_effects collapsed_effects n/a
  • File
highest_impact_effects highest_impact_effects n/a
  • File
processed_variants_collection processed_variants_collection n/a
  • File
variants_for_plotting variants_for_plotting n/a
  • File
variant_frequency_plot variant_frequency_plot n/a
  • File
combined_variant_report combined_variant_report n/a
  • File
by_variant_report by_variant_report n/a
  • File

Version History

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

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Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

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help Creators and Submitter
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Wolfgang Maier

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Views: 1342   Downloads: 232

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

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