Add feature/species specific params by sgsutcliffe · Pull Request #42 · phac-nml/staramrnf

sgsutcliffe · 2026-06-10T19:20:18Z

Update starAMR parameters

Add parameters for starAMR module

Parameters used in starAMR now modifiable in the config for the module.

        minimum_N50_value                    = 10000
        minimum_contig_length                = 300
        unacceptable_number_contigs          = 1000
        pid_threshold                        = 98
        percent_length_overlap_plasmidfinder = 60       
        no_exclude_genes                     = false
        exclude_negatives                    = false
        exclude_resistance_phenotypes        = false

Add species specific starAMR parameters

Parameters that use the species classification to assign the values (can be turned off through --skip_species_classification . The defaults are:

--genome_size_lower_bound : 4000000
--genome_size_upper_bound : 6000000
--percent_length_overlap_resfinder : 60
--percent_length_overlap_pointfinder : 95

The species with specific settings are:

Salmonella, Shigella, or Escherchia coli

Lower bound for our genome size for quality metrics = 4,000,000
Upper bound for our genome size for quality metrics= 6,700,000
Percent length overlap of BLAST hit for ResFinder Database = 52
PointFinder Database = Salmonella or PointFinder Database = E.coli

Campylobacter

Lower bound for our genome size for quality metrics= 1,250,000
Upper bound for our genome size for quality metrics= 2,500,000
Percent length overlap of BLAST hit for ResFinder Database = 52
Percent length overlap ofBLAST hit for PointFinder Database = 58
Point Finder Database = Campylobacter

0.1.0 Release

Minor Release: 0.2.0

Minor Release: 0.3.0

Release: 0.3.1

Patch Release: 0.3.2

Patch Release: 0.3.3

emarinier · 2026-06-12T15:16:39Z

+            // Ecoli with wrong species in samplesheet
            assert path("$outputDir/staramr/B2_results/B2_settings.staramr.txt").exists()
            def ecoli_settings = new File("$outputDir/staramr/B2_results/B2_settings.staramr.txt")
            def ecoli_cmd = ecoli_settings.readLines().get(0)
-            assert ecoli_cmd == "command_line                  = /usr/local/bin/staramr search --pointfinder-organism escherichia_coli --minimum-contig-length 300 --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000 --pid-threshold 98 --percent-length-overlap-plasmidfinder 60 --percent-length-overlap-resfinder 60 --percent-length-overlap-pointfinder 95 --nprocs 1 -o B2_results B2.fasta"
+            assert ecoli_cmd == "command_line                  = /usr/local/bin/staramr search --pointfinder-organism escherichia_coli --minimum-contig-length 300 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000 --pid-threshold 98 --percent-length-overlap-plasmidfinder 60 --genome-size-lower-bound 4000000 --genome-size-upper-bound 6700000 --percent-length-overlap-resfinder 52 --percent-length-overlap-pointfinder 95 --nprocs 1 -o B2_results B2.fasta"


Can you explain what this is testing and how it works?

The sample sheet is:

sample,sample_name,contigs,species GCA_000008105,A 1#,https://github.com/phac-nml/staramrnf/raw/dev/tests/genomes/salmonella/GCA_000008105.1_ASM810v1_genomic.fna.gz,Salmonella GCA_000947975,B2,https://github.com/phac-nml/staramrnf/raw/dev/tests/genomes/ecoli/GCA_000947975.1_ASM94797v1_genomic.fna.gz,Escherichia coli GCF_000196035,B2,https://github.com/phac-nml/staramrnf/raw/dev/tests/genomes/listeria/GCF_000196035.1_ASM19603v1_genomic.fna,Listeria monocytogenes GCF_000196035_B,,https://github.com/phac-nml/staramrnf/raw/dev/tests/genomes/listeria/GCF_000196035.1_ASM19603v1_genomic.fna,Listeria monocytogenes

Where there are 2 B2 sample_name entries, one is E coli (GCA_000947975) and the other is Listeria (GCF_000196035).

Is the test checking the Listeria one or the E. coli one? I don't really understand which one the B2_results is supposed to be corresponding to. If it corresponds to the E. coli one, why is E. coli the wrong species in the sample sheet? It looks like there's Escherichia coli in the sample sheet for GCA_000947975,B2. Is it not actually E. coli?

The change I made is simply because the new feature changes the output, and so I adjusted it for the test.

As for the test itself, I believe this original test was slightly poorly planned (my first pipeline) test that was a kind of all-in-one where it was confirming the sample renaming and the outputs of these for a full test.

Not sure why the last sample is not tested. Maybe it is a good time to fix things up.

emarinier · 2026-06-12T15:23:28Z

    validationFailUnrecognisedParams = false
    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
+    validationSchemaIgnoreParams     = 'genomes,igenomes_base,genus_list,default_staramr,salmonella,escherichia,shigella,campylobacter'


What are the warnings or errors when not ignored?

It looks like this at the top of every run. Since they are more "settings" than "parameters" I decided to hide them:
e.g,

N E X T F L O W ~ version 24.10.6 Launching `main.nf` [amazing_engelbart] DSL2 - revision: 38dd4bef6a WARN: The following invalid input values have been detected: * --genus_list: [salmonella, campylobacter, escherichia, shigella] * --default_staramr: [genome_size_lower_bound:4000000, genome_size_upper_bound:6000000, percent_length_overlap_resfinder:60, percent_length_overlap_pointfinder:95] * --salmonella: [genome_size_lower_bound:4000000, genome_size_upper_bound:6700000, percent_length_overlap_resfinder:52, percent_length_overlap_pointfinder:95] * --escherichia: [genome_size_lower_bound:4000000, genome_size_upper_bound:6700000, percent_length_overlap_resfinder:52, percent_length_overlap_pointfinder:95] * --shigella: [genome_size_lower_bound:4000000, genome_size_upper_bound:6700000, percent_length_overlap_resfinder:52, percent_length_overlap_pointfinder:95] * --campylobacter: [genome_size_lower_bound:1250000, genome_size_upper_bound:2500000, percent_length_overlap_resfinder:52, percent_length_overlap_pointfinder:58]

emarinier · 2026-06-12T15:25:01Z

+### Genus specific settings
+
+They are used when the `species` column has any of the following genus selected:
+```
+genus_list = ['salmonella', 'campylobacter', 'escherichia', 'shigella']
+```


### Genus-specific settings Genus-specific settings are used when the `species` column of the sample sheet contains any of the following genera:

emarinier · 2026-06-12T15:26:59Z

+
+
+


Possibly too much whitespace

emarinier · 2026-06-12T15:27:31Z

+- Upper bound for our genome size for quality metrics= 2,500,000
+- Percent length overlap of BLAST hit for ResFinder Database = 52 
+- Percent length overlap ofBLAST hit for PointFinder Database = 58
+- Point Finder Database = Campylobacter


PointFinder (no space)

emarinier · 2026-06-12T15:27:47Z

+- Lower bound for our genome size for quality metrics= 1,250,000
+- Upper bound for our genome size for quality metrics= 2,500,000
+- Percent length overlap of BLAST hit for ResFinder Database = 52 
+- Percent length overlap ofBLAST hit for PointFinder Database = 58


of BLAST (space)

emarinier · 2026-06-12T15:28:22Z

+- Lower bound for our genome size for quality metrics = 4,000,000
+- Upper bound for our genome size for quality metrics= 6,700,000 
+- Percent length overlap of BLAST hit for ResFinder Database = 52
+- PointFinder Database = Salmonella or PointFinder Database = E.coli
+#### Campylobacter
+- Lower bound for our genome size for quality metrics= 1,250,000
+- Upper bound for our genome size for quality metrics= 2,500,000


Some = have space before, others do not. Recommend making consistent.

sgsutcliffe and others added 12 commits August 14, 2024 11:57

Merge pull request #23 from phac-nml/dev

61de9f9

0.1.0 Release

Merge pull request #29 from phac-nml/dev

6446c91

Minor Release: 0.2.0

Merge pull request #32 from phac-nml/dev

2b4d656

Minor Release: 0.3.0

Merge pull request #35 from phac-nml/dev

09000db

Release: 0.3.1

Merge pull request #38 from phac-nml/dev

ae8fed8

Patch Release: 0.3.2

Merge pull request #41 from phac-nml/dev

4feb3be

Patch Release: 0.3.3

Add genus specific params

e388c85

Fix pre-exisiting tests

ef1774d

Add tests for new feature

6884930

ignore pseudo-parameters

3a9a01d

Add documentation

7be3d46

Add documentation-fix link

0f44c5c

emarinier requested changes Jun 12, 2026

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Fix up typos

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Add feature/species specific params#42

Add feature/species specific params#42
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sgsutcliffe commented Jun 10, 2026

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sgsutcliffe commented Jun 10, 2026

Update starAMR parameters

Add parameters for starAMR module

Add species specific starAMR parameters

Salmonella, Shigella, or Escherchia coli

Campylobacter

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