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.
  • 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 use 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://doi.org/10.5281/zenodo.4555734
  • File

Steps

ID Name Description
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
prefiltered_variants prefiltered_variants n/a
  • File
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
af_recalculated af_recalculated n/a
  • File
collapsed_effects collapsed_effects n/a
  • File
highest_impact_effects highest_impact_effects n/a
  • File
cleaned_header cleaned_header n/a
  • File
processed_variants_collection processed_variants_collection n/a
  • File
all_variants_all_samples all_variants_all_samples 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

v0.3 (latest) Created 15th Oct 2022 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 18aba04

v0.2 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
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Activity

Views: 6900   Downloads: 1013

Created: 12th Mar 2021 at 13:41

Last updated: 15th Oct 2022 at 03:01

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