Workflow Type: Galaxy
Frozen
Frozen
Microbiome - Variant calling and Consensus Building
Inputs
ID | Name | Description | Type |
---|---|---|---|
collection_of_preprocessed_samples | collection_of_preprocessed_samples | Output collection from the Nanopore Preprocessing workflow |
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reference_genome_of_tested_strain | reference_genome_of_tested_strain | Can be built in the tool later |
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samples_profile | samples_profile | based on the lab preparation of the samples during sequencing, there should be a sample profile better than the other, to be chosen as an optional input to Minimap2. e.g. PacBio/Oxford Nanpore For more details check: https://github.com/lh3/minimap2?tab=readme-ov-file#use-cases |
|
Steps
ID | Name | Description |
---|---|---|
3 | Convert compressed file to uncompressed. | CONVERTER_gz_to_uncompressed |
4 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 |
5 | Clair3 | toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1 |
6 | Samtools depth | toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2 |
7 | Samtools coverage | toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2 |
8 | bcftools norm | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy4 |
9 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2 |
10 | Remove beginning | Remove beginning1 |
11 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
12 | Table Compute | toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 |
13 | Cut | Cut1 |
14 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
15 | bcftools consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4 |
16 | Select first | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 |
17 | Remove beginning | Remove beginning1 |
18 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
19 | Count | Count1 |
20 | Advanced Cut | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2 |
21 | Cut | Cut1 |
22 | Paste | Paste1 |
23 | Select first | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 |
24 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
25 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
decompressed_rg_file | decompressed_rg_file | n/a |
|
map_with_minimap2 | map_with_minimap2 | n/a |
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clair3_full_alignment_vcf | clair3_full_alignment_vcf | n/a |
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clair3_pileup_vcf | clair3_pileup_vcf | n/a |
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clair3_merged_output | clair3_merged_output | n/a |
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normalized_vcf_output | normalized_vcf_output | n/a |
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quality_filtered_vcf_output | quality_filtered_vcf_output | n/a |
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extracted_fields_from_the_vcf_output | extracted_fields_from_the_vcf_output | n/a |
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bcftools_consensus | bcftools_consensus | n/a |
|
mapping_coverage_percentage_per_sample | mapping_coverage_percentage_per_sample | n/a |
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mapping_mean_depth_per_sample | mapping_mean_depth_per_sample | n/a |
|
number_of_variants_per_sample | number_of_variants_per_sample | n/a |
|
Version History
v0.1.2 (latest) Created 30th Oct 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1.2
Frozen
v0.1.2
a9ee521
v0.1 (earliest) Created 26th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
4018be7
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Created: 26th Jun 2024 at 03:02
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