influenza-isolates-consensus-and-subtyping/main

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Workflow Type: Galaxy

This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.

SEEK ID: https://workflowhub.eu/workflows/1260?version=2

Inputs

ID Name Description Type
References per segment collection References per segment collection A collection of influenza A reference sequences organized by segment
  • File[]
Sequenced paired-end data Sequenced paired-end data Paired collection of forward and reverse reads of the sequenced isolate
  • File[]

Steps

ID Name Description
2 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
3 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
4 Line/Word/Character count wc_gnu
5 Unzip collection __UNZIP_COLLECTION__
6 Parse parameter value param_value_from_file
7 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
8 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
9 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
10 Run IQ-Tree (at least 3 samples) toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
11 Multiple sequences flag toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
12 Apply rules __APPLY_RULES__
13 Relabel identifiers __RELABEL_FROM_FILE__
14 VAPOR toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3
15 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
16 Select first Show beginning1
17 seqtk_subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0
18 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
19 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
20 Extract dataset __EXTRACT_DATASET__
21 Select Grep1
22 Select Grep1
23 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
24 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
25 Paste Paste1
26 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18
27 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
28 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
29 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
30 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
31 Split BAM by reference toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy2
32 Apply rules __APPLY_RULES__
33 Relabel identifiers __RELABEL_FROM_FILE__
34 Apply rules __APPLY_RULES__
35 ivar consensus toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0
36 Apply rules __APPLY_RULES__
37 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
38 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
39 MAFFT toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0
40 Pick parameter value toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
41 IQ-TREE toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.3.3+galaxy0
42 snipit toolshed.g2.bx.psu.edu/repos/iuc/snipit/snipit/1.2+galaxy0

Outputs

ID Name Description Type
fastp reports fastp reports n/a
  • File
Vapor - closest references Vapor - closest references n/a
  • File
Hybrid reference genomes used for mapping Hybrid reference genomes used for mapping n/a
  • File
Final read mapping results Final read mapping results n/a
  • File
Subtyping results Subtyping results n/a
  • File
QC reports for mapping results QC reports for mapping results n/a
  • File
Per-sample consensus sequences Per-sample consensus sequences n/a
  • File
Per-segment consensus sequences with samples combined Per-segment consensus sequences with samples combined n/a
  • File
Multiple sequence alignments per segment Multiple sequence alignments per segment n/a
  • File
IQ-Tree per-segment ML tree IQ-Tree per-segment ML tree n/a
  • File
IQ-Tree per-segment ML distance matrix IQ-Tree per-segment ML distance matrix n/a
  • File
IQ-Tree per-segment report IQ-Tree per-segment report n/a
  • File
Snipit plots per segment Snipit plots per segment n/a
  • File

Version History

v0.2 (latest) Created 14th May 2025 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 d33f57b

v0.1 (earliest) Created 29th Jan 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 70af6f3
help Creators and Submitter
Creators
Submitter
Tools
fastp
VAPOR
seqtk
BWA
SAMtools
QualiMap
BamTools
MAFFT
iqtree
snipit
License
GNU Affero General Public License v3.0 or later (AGPL-3.0-or-later)
Activity

Views: 2328   Downloads: 3049   Runs: 0

Created: 29th Jan 2025 at 03:01

Last updated: 18th Aug 2025 at 18:50

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