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 #main/AF Filter Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the report.
  • float
DP Filter #main/DP Filter Depth Filter. This is the minimum depth of all alignments at a variant site.
  • int
DP_ALT Filter #main/DP_ALT Filter Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.
  • int
Number of Clusters #main/Number of Clusters Number of Clusters to find in Variant Frequency Plot.
  • int
Variation data to report #main/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
  • array containing
    • File
gene products translations #main/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
by_variant_report #main/by_variant_report n/a
  • File
collapsed_effects #main/collapsed_effects n/a
  • File
combined_variant_report #main/combined_variant_report n/a
  • File
filtered_and_renamed_effects #main/filtered_and_renamed_effects n/a
  • File
filtered_extracted_variants #main/filtered_extracted_variants n/a
  • File
filtered_variants #main/filtered_variants n/a
  • File
highest_impact_effects #main/highest_impact_effects n/a
  • File
processed_variants_collection #main/processed_variants_collection n/a
  • File
variant_frequency_plot #main/variant_frequency_plot n/a
  • File
variants_for_plotting #main/variants_for_plotting 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: 621   Downloads: 10

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

Last used: 5th Dec 2022 at 08:36

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