Workflow Type: Galaxy
Frozen
Frozen
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. |
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DP Filter | #main/DP Filter | Depth Filter. This is the minimum depth of all alignments at a variant site. |
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DP_ALT Filter | #main/DP_ALT Filter | Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant. |
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Number of Clusters | #main/Number of Clusters | Number of Clusters to use in Variant Frequency Plot. |
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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 |
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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 |
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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 |
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af_recalculated | #main/af_recalculated | n/a |
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all_variants_all_samples | #main/all_variants_all_samples | n/a |
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by_variant_report | #main/by_variant_report | n/a |
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collapsed_effects | #main/collapsed_effects | n/a |
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combined_variant_report | #main/combined_variant_report | n/a |
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dp_alt_filter_threshold | #main/dp_alt_filter_threshold | n/a |
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dp_filter_threshold | #main/dp_filter_threshold | n/a |
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filtered_and_renamed_effects | #main/filtered_and_renamed_effects | n/a |
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filtered_extracted_variants | #main/filtered_extracted_variants | n/a |
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filtered_variants | #main/filtered_variants | n/a |
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highest_impact_effects | #main/highest_impact_effects | n/a |
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plot_number_of_clusters | #main/plot_number_of_clusters | n/a |
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prefiltered_variants | #main/prefiltered_variants | n/a |
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variant_frequency_plot | #main/variant_frequency_plot | n/a |
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variants_for_plotting | #main/variants_for_plotting | n/a |
|
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
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 13 files
Frozen
master
7ce82db
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
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