Workflow Type: Galaxy

This workflow takes a VCF dataset 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 lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.

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 reports.
  • 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 use 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://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_column1/2.0
13 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
14 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
15 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
16 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
17 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
18 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
19 Filter Filter1
20 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
21 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
22 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
23 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
24 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
25 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
26 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
27 Cut Cut1
28 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
29 Cut Cut1
30 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4
31 Cut Cut1
32 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
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
af_filter_threshold #main/af_filter_threshold n/a
  • File
af_recalculated #main/af_recalculated n/a
  • File
all_variants_all_samples #main/all_variants_all_samples n/a
  • File
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
dp_alt_filter_threshold #main/dp_alt_filter_threshold n/a
  • File
dp_filter_threshold #main/dp_filter_threshold 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
plot_number_of_clusters #main/plot_number_of_clusters n/a
  • File
prefiltered_variants #main/prefiltered_variants 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

v0.3.4 (latest) Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v0.3.4


Frozen v0.3.4 8f39392

v0.3.3 Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v0.3.3


Frozen v0.3.3 0b69554

v0.3.1 Created 7th Oct 2024 at 16:31 by WorkflowHub Bot

Updated to v0.3.1


Frozen v0.3.1 b3c2ba3

v0.3 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
Creator
Additional credit

Wolfgang Maier

Submitter
License
Activity

Views: 8996   Downloads: 1626   Runs: 1

Created: 12th Mar 2021 at 13:41

Last updated: 3rd Oct 2024 at 03:02

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 240 KB
Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH