AMR detection workflow - CFIA

Annotation:

StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: BBTools: BBduk
List of dataset pairs
Output dataset 'output' from step 1
No reference
Advanced options:
27
True
True
1
0.0
0.0
0
0
0
False
False
False
False
False
Unmatched Matched Single
No
No
Step 3: Shovill
Paired End
Output dataset 'outputu' from step 2
Output dataset 'outputu2' from step 2
False
skesa
Advanced options:
contig%05d
100
Empty.
Empty.
Empty.
No corrections
0
2
True
Step 4: Shovill
Paired End
Output dataset 'outputu' from step 2
Output dataset 'outputu2' from step 2
False
Spades
Advanced options:
contig%05d
100
Empty.
Empty.
Empty.
No corrections
0
2
True
Step 5: pilon
Use a genome from history
Output dataset 'contigs' from step 3
False
False
False
Use default options
Step 6: pilon
Use a genome from history
Output dataset 'contigs' from step 4
False
False
False
Use default options
Step 7: MOB-Recon
Output dataset 'output_fasta' from step 5
Advanced parameters:
True
True
False
1e-05
1e-05
1e-05
1e-05
1000
80
80
80
80
80
80
60
80
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
Step 8: MOB-Recon
Output dataset 'output_fasta' from step 6
Advanced parameters:
True
True
False
1e-05
1e-05
1e-05
1e-05
1000
80
80
80
80
80
80
60
80
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
select at runtime
Step 9: sistr_cmd
Output dataset 'chromosome' from step 7
Tabular (tab-delimited values)
False
True
False
True
Basic results only
False
Show info messages
Step 10: hamronize
Output dataset 'output_prediction_tab' from step 9
abricate
tsv
Empty.
Empty.
Step 11: hamronize: summarize
Output dataset 'output_tsv' from step 10
tsv