mgnify-amplicon-pipeline-v5-rrna-prediction/main

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Classification and visualization of SSU, LSU sequences.

SEEK ID: https://workflowhub.eu/workflows/1270?version=2

Inputs

ID Name Description Type
Clan information file Clan information file This file lists which models belong to the same clan.
  • File
Processed sequences Processed sequences Post quality control.
  • File[]

Steps

ID Name Description
2 cmsearch toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.5+galaxy0
3 Filter empty datasets __FILTER_EMPTY_DATASETS__
4 CMsearch deoverlap toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy2
5 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
6 SSU BED forward toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
7 SSU BED reverse toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
8 LSU BED forward toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
9 LSU BED reverse toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
10 SSU BED toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
11 LSU BED toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
12 Filter empty datasets __FILTER_EMPTY_DATASETS__
13 Filter empty datasets __FILTER_EMPTY_DATASETS__
14 Concatenate toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
15 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
16 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
17 Filter collection __FILTER_FROM_FILE__
18 Filter collection __FILTER_FROM_FILE__
19 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0
20 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0
21 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
22 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
23 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
24 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
25 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
26 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
27 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
28 Filter empty datasets __FILTER_EMPTY_DATASETS__
29 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
30 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
31 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
32 Filter empty datasets __FILTER_EMPTY_DATASETS__
33 Filter empty datasets __FILTER_EMPTY_DATASETS__
34 Filter empty datasets __FILTER_EMPTY_DATASETS__
35 Filter empty datasets __FILTER_EMPTY_DATASETS__
36 Map empty/not empty collection to boolean n/a
37 Filter empty datasets __FILTER_EMPTY_DATASETS__
38 Filter empty datasets __FILTER_EMPTY_DATASETS__
39 Filter empty datasets __FILTER_EMPTY_DATASETS__
40 Map empty/not empty collection to boolean n/a
41 Map empty/not empty collection to boolean n/a
42 Krona SSU SILVA toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
43 Map empty/not empty collection to boolean n/a
44 Krona LSU SILVA toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
45 HDF5 SSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
46 JSON SSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
47 HDF5 LSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
48 JSON LSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1

Outputs

ID Name Description Type
LSU and SSU BED regions LSU and SSU BED regions n/a
  • File
SSU FASTA files SSU FASTA files n/a
  • File
LSU FASTA files LSU FASTA files n/a
  • File
SSU taxonomic classifications using SILVA DB SSU taxonomic classifications using SILVA DB n/a
  • File
SSU OTU tables (SILVA DB) SSU OTU tables (SILVA DB) n/a
  • File
LSU taxonomic classifications using SILVA DB LSU taxonomic classifications using SILVA DB n/a
  • File
LSU OTU tables (SILVA DB) LSU OTU tables (SILVA DB) n/a
  • File
SSU taxonomic abundance pie charts (SILVA DB) SSU taxonomic abundance pie charts (SILVA DB) n/a
  • File
LSU taxonomic abundance pie charts (SILVA DB) LSU taxonomic abundance pie charts (SILVA DB) n/a
  • File
SSU OTU tables in HDF5 format (SILVA DB) SSU OTU tables in HDF5 format (SILVA DB) n/a
  • File
SSU OTU tables in JSON format (SILVA DB) SSU OTU tables in JSON format (SILVA DB) n/a
  • File
LSU OTU tables in HDF5 format (SILVA DB) LSU OTU tables in HDF5 format (SILVA DB) n/a
  • File
LSU OTU tables in JSON format (SILVA DB) LSU OTU tables in JSON format (SILVA DB) n/a
  • File

Version History

v0.2 (latest) Created 26th Mar 2025 at 09:52 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 50103bf

v0.1 (earliest) Created 4th Feb 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 5807372
help Creators and Submitter
Creators
Additional credit

EMBL's European Bioinformatics Institute

Submitter
Tools
Infernal
cmsearch-deoverlap
bx-python
BEDTools
FASTX-Toolkit
MAPseq
taxonomy_krona_chart
biomformat
License
Apache License 2.0 (Apache-2.0)
Activity

Views: 2390   Downloads: 3108   Runs: 2

Created: 4th Feb 2025 at 03:01

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