influenza-isolates-consensus-and-subtyping/main v0.1
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Workflow Type: Galaxy
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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 | 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 |
|
| Vapor - closest references | Vapor - closest references | 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 |
|
| Subtyping results | Subtyping 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 |
|
| IQ-Tree per-segment ML tree | IQ-Tree per-segment ML tree | n/a |
|
| IQ-Tree per-segment ML distance matrix | IQ-Tree per-segment ML distance matrix | n/a |
|
| IQ-Tree per-segment report | IQ-Tree per-segment report | n/a |
|
| Snipit plots per segment | Snipit plots per segment | 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
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