influenza-isolates-consensus-and-subtyping/main
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Workflow Type: Galaxy
Frozen
Tests 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 |
|
| Sequenced paired-end data | Sequenced paired-end data | Paired collection of forward and reverse reads of the sequenced isolate |
|
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 |
|
| fastp reports | fastp reports | n/a |
|
| successful VAPOR runs - closest references | successful VAPOR runs - closest references | n/a |
|
| Subtyping results | Subtyping results | n/a |
|
| Hybrid reference genomes used for mapping | Hybrid reference genomes used for mapping | n/a |
|
| Final read mapping_results | Final read mapping_results | n/a |
|
| QC reports for mapping results | QC reports for mapping results | n/a |
|
| Per-sample consensus sequences | Per-sample consensus sequences | n/a |
|
| Per-segment consensus sequences with samples combined | Per-segment consensus sequences with samples combined | n/a |
|
| Multiple sequence alignments per segment | Multiple sequence alignments per segment | n/a |
|
| Snipit plots per segment | Snipit plots per segment | n/a |
|
| IQ-Tree per-segment ML tree | IQ-Tree per-segment ML tree | n/a |
|
| IQ-Tree per-segment report | IQ-Tree per-segment report | n/a |
|
| IQ-Tree per-segment ML distance matrix | IQ-Tree per-segment ML distance matrix | n/a |
|
Version History
v0.1 (earliest) Created 29th Jan 2025 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.170af6f3
Creators and Submitter
Activity
Views: 875 Downloads: 133 Runs: 0
Created: 29th Jan 2025 at 03:01
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