This is an aggregation of the work done in Seq4AMR consisting of the following workflows:
- WF1: AbritAMR / AMRFinderPlus
- WF2: Sciensano (not currently included)
- WF3: SRST2
- WF4: StarAMR
Installation
- You will need to:
- run the RGI Database Builder as a Galaxy admin (if this hasn't been done already)
- Have the en_US.UTF-8 locale installed on the compute nodes executing cast/melt jobs.
- Install the requisite tools with e.g.
shed-tools
command from theephemeris
suite:shed-tools install -g https://galaxy.example.com -a API_KEY -t tools.yaml
(tools.yaml is provided in this repository.)
- Then you can import this workflow
- Navigate to
/workflows/import
of your Galaxy server - Select "GA4GH servers"
- Enter
name:"AMR-Pathfinder"
- Navigate to
- And run it
- You must provide a Sequencing collection (list:paired of fastq files)
- And a Genomes collection (list of fasta files)
- Both of these should use identical collection element identifiers
Outputs
This will produce two important tables: "Binary Comparison" and a "% Identity Scored Outputs".
Binary comparison
This file reports the discovery or absence of specific AMR genes across all tested AMR Analysis tools. You will mostly see 1s (presence) or 0s (absence) but you may occasionally see higher numbers when an AMR tool reports multiple hits for a specific gene.
% Identity Scored Outputs
This is similar to binary comparison, but using the % identity reported by each AMR tool. For cases where multiple hits were detected, we take the highest.
Known Issues
The names for identified AMR genes is highly inconsistent across AMR analysis tools. We urge the AMR community to rectify this by standardising gene names used in their tooling.
Steps
ID | Name | Description |
---|---|---|
5 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
6 | Sanitise Filename | n/a |
7 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
8 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
9 | benchAMRking: wf1 | n/a |
10 | benchAMRking: wf3b | n/a |
11 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
12 | Add column | addValue |
13 | Add column | addValue |
14 | Relabel identifiers | __RELABEL_FROM_FILE__ |
15 | WF3: SRST2 :: AMR - SeqSero2/SISTR | n/a |
16 | Shovill | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1 |
17 | Add column | addValue |
18 | ABRicate | toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 |
19 | staramr | toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1 |
20 | Select | Grep1 |
21 | hamronize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1 |
22 | hamronize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1 |
23 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
24 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
25 | hamronize summarize: | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.1.4+galaxy0 |
26 | hamronize: summarize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2 |
27 | hamronize: summarize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2 |
28 | Select | Grep1 |
29 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2 |
30 | Cut | Cut1 |
31 | Select | Grep1 |
32 | Add column | addValue |
33 | Merge collections | __MERGE_COLLECTION__ |
34 | Apply rules | __APPLY_RULES__ |
35 | Concatenate multiple datasets | toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3 |
36 | Move WF# col to second position, keep score | Cut1 |
37 | Move WF# col to second position 2, delete score | Cut1 |
38 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
39 | Add column | addValue |
40 | Concatenate datasets | cat1 |
41 | Concatenate datasets | cat1 |
42 | % Identity | toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2 |
43 | Binary Comparison | toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2 |
Version History
Version 4.7 (latest) Created 14th Nov 2024 at 14:57 by Helena Rasche
Sanitise filenames for input collections
Open
master
9d84881
Version 4.6 (earliest) Created 28th Oct 2024 at 13:43 by Helena Rasche
Initial working version of the AMR Pathfinder project workflow
Frozen
Version-4.6
a29814d
Creators
Submitter
Views: 763 Downloads: 75 Runs: 8
Created: 28th Oct 2024 at 13:43
Last updated: 4th Nov 2024 at 15:04