allele-based-pathogen-identification/main

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Workflow Type: Galaxy

Microbiome - Variant calling and Consensus Building

SEEK ID: https://workflowhub.eu/workflows/1063?version=4

Inputs

ID Name Description Type
collection_of_preprocessed_samples collection_of_preprocessed_samples Output collection from the Nanopore Preprocessing workflow
  • File[]
reference_genome_of_tested_strain reference_genome_of_tested_strain Can be built in the tool later
  • File
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
  • string?

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+galaxy1
5 Clair3 toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+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+galaxy1
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
  • File
map_with_minimap2 map_with_minimap2 n/a
  • File
clair3_full_alignment_vcf clair3_full_alignment_vcf n/a
  • File
clair3_pileup_vcf clair3_pileup_vcf n/a
  • File
clair3_merged_output clair3_merged_output n/a
  • File
normalized_vcf_output normalized_vcf_output n/a
  • File
quality_filtered_vcf_output quality_filtered_vcf_output n/a
  • File
extracted_fields_from_the_vcf_output extracted_fields_from_the_vcf_output n/a
  • File
bcftools_consensus bcftools_consensus n/a
  • File
mapping_coverage_percentage_per_sample mapping_coverage_percentage_per_sample n/a
  • File
mapping_mean_depth_per_sample mapping_mean_depth_per_sample n/a
  • File
number_of_variants_per_sample number_of_variants_per_sample n/a
  • File

Version History

v0.1.4 (latest) Created 26th Mar 2025 at 12:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 cd3bd9f

v0.1.3 Created 26th Mar 2025 at 12:01 by WorkflowHub Bot

Updated to v0.1.3


Frozen v0.1.3 08df928

v0.1.2 Created 30th Oct 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 a9ee521

v0.1.1 Created 4th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 f495c88

v0.1 (earliest) Created 26th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 4018be7
help Creators and Submitter
Creators
  • Engy Nasr
  • Bérénice Batut
  • Paul Zierep
Submitter
Tools
Minimap2
Clair3
SAMtools
BCFtools
License
MIT License (MIT)
Activity

Views: 7219   Downloads: 42609   Runs: 0

Created: 26th Jun 2024 at 03:02

Last updated: 26th Mar 2025 at 10:06

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