influenza-isolates-consensus-and-subtyping/main
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v0.3 (latest)

v0.2

v0.1 (earliest)

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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.

SEEK ID: https://workflowhub.eu/workflows/1260?version=3

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+galaxy3
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/1.1.0+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	Apply rules	__APPLY_RULES__
15	Relabel identifiers	__RELABEL_FROM_FILE__
16	VAPOR	toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.3+galaxy0
17	Filter failed datasets	__FILTER_FAILED_DATASETS__
18	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
19	Select first	Show beginning1
20	seqtk_subseq	toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.5+galaxy0
21	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
22	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
23	Select	Grep1
24	Select	Grep1
25	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
26	Paste	Paste1
27	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
28	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
29	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__
30	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
31	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1
32	Split BAM by reference	toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy2
33	QualiMap BamQC	toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0
34	Apply rules	__APPLY_RULES__
35	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
36	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
37	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
38	Relabel identifiers	__RELABEL_FROM_FILE__
39	Apply rules	__APPLY_RULES__
40	Extract element identifiers	toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
41	ivar consensus	toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0
42	Line/Word/Character count	wc_gnu
43	Apply rules	__APPLY_RULES__
44	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
45	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
46	Filter	Filter1
47	Filter	Filter1
48	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3
49	Cut	Cut1
50	Cut	Cut1
51	Filter collection	__FILTER_FROM_FILE__
52	MAFFT	toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy2
53	Filter collection	__FILTER_FROM_FILE__
54	snipit	toolshed.g2.bx.psu.edu/repos/iuc/snipit/snipit/1.7+galaxy0
55	IQ-TREE	toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1

Outputs

ID	Name	Description	Type
fastp reports	fastp reports	n/a	File
fastp-processed paired collection	fastp-processed paired collection	n/a	File
successful VAPOR runs - closest references	successful VAPOR runs - closest references	n/a	File
Hybrid reference genomes used for mapping	Hybrid reference genomes used for mapping	n/a	File
Subtyping results	Subtyping results	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 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
IQ-Tree per-segment ML tree	IQ-Tree per-segment ML tree	n/a	File