Workflow Type: Galaxy

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

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 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy1
3 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
4 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
5 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.1+galaxy0
6 Line/Word/Character count wc_gnu
7 Line/Word/Character count wc_gnu
8 Unzip collection __UNZIP_COLLECTION__
9 Parse parameter value param_value_from_file
10 Parse parameter value param_value_from_file
11 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
12 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
13 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
14 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
15 Relabel identifiers __RELABEL_FROM_FILE__
16 Apply rules __APPLY_RULES__
17 Duplicate file to collection __DUPLICATE_FILE_TO_COLLECTION__
18 Relabel identifiers __RELABEL_FROM_FILE__
19 Apply rules __APPLY_RULES__
20 VAPOR toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3
21 Flatten collection __FLATTEN__
22 Relabel identifiers __RELABEL_FROM_FILE__
23 Filter failed datasets __FILTER_FAILED_DATASETS__
24 Flatten collection __FLATTEN__
25 Apply rules This seemingly no-op transformation will remove samples with no remaining segment results (cases where vapor failed for every segment). __APPLY_RULES__
26 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
27 Select first Show beginning1
28 Flatten collection __FLATTEN__
29 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
30 Merge collections __MERGE_COLLECTION__
31 Select Grep1
32 Select Grep1
33 Harmonize two collections __HARMONIZELISTS__
34 Paste Paste1
35 Apply rules __APPLY_RULES__
36 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
37 seqtk_subseq toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0
38 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy0
39 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
40 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
41 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0
42 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
43 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
44 Filter failed datasets bwa mem will fail if no reference for any segment got suggested by vapor, i.e. the reference genome is empty. In that case, we need to skip further analysis of the sample. __FILTER_FAILED_DATASETS__
45 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3
46 Split BAM by reference toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy2
47 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0
48 Apply rules __APPLY_RULES__
49 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
50 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
51 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
52 Relabel identifiers __RELABEL_FROM_FILE__
53 Apply rules __APPLY_RULES__
54 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
55 ivar consensus toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0
56 Line/Word/Character count wc_gnu
57 Apply rules __APPLY_RULES__
58 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
59 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
60 Filter Filter1
61 Filter Filter1
62 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
63 Cut Cut1
64 Cut Cut1
65 Filter collection __FILTER_FROM_FILE__
66 MAFFT toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy1
67 Filter collection __FILTER_FROM_FILE__
68 snipit toolshed.g2.bx.psu.edu/repos/iuc/snipit/snipit/1.6+galaxy0
69 IQ-TREE toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy0

Outputs

ID Name Description Type
fastp-processed paired collection fastp-processed paired collection n/a
  • File
fastp reports fastp reports n/a
  • File
successful VAPOR runs - closest references successful VAPOR runs - closest references n/a
  • File
Subtyping results Subtyping results 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
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
Snipit plots per segment Snipit plots per segment n/a
  • File
IQ-Tree per-segment ML tree IQ-Tree per-segment ML tree n/a
  • File
IQ-Tree per-segment report IQ-Tree per-segment report n/a
  • File
IQ-Tree per-segment ML distance matrix IQ-Tree per-segment ML distance matrix 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
  • Wolfgang Maier
  • Viktoria Isabel Schwarz
Submitter
Activity

Views: 875   Downloads: 133   Runs: 0

Created: 29th Jan 2025 at 03:01

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 161 KB
Powered by
(v.1.16.0)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH