Add sylph

[stephenturner]

This PR adds sylph (https://github.com/bluenote-1577/sylph). sylph is a program that can perform ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

Hi Dr. T, thanks for the PR! I'm excited to see you contribute here.

Myself or one of the other maintainers will review when we are able and make suggestions and/or request changes.

I just approved the CI workflow to run, so that will test that the image builds OK. Looks like it already passed successfully 👍

Upon a glance everything looks great, but when I get a chance I'll take a closer look.

Nice to see a rust base image in use here! I don't have a ton of experience with building rust packages so this will be a learning opportunity for me

[erinyoung]

I think this looks great!

I like the builder stage (which makes for a smaller image), and I like the test stage is using actual files.

I made two adjustments:

1. I changed the hyperlink in the README to point to dockerhub (where the sylph image would be)
2. I added in a sylph -h line to the test stage - just to make sure it's in PATH

[erinyoung]

There is one warning during compiling. Is this something that can be ignored?

#10 50.29    Compiling sylph v0.4.1 (/sylph-0.4.1)
#10 50.84 warning: call to `.clone()` on a reference in this situation does nothing
#10 50.84    --> src/contain.rs:485:47
#10 50.84     |
#10 50.84 485 |         let file = File::open(read_sketch_file.clone()).expect(&format!(
#10 50.84     |                                               ^^^^^^^^ help: remove this redundant call
#10 50.84     |
#10 50.84     = note: the type `str` does not implement `Clone`, so calling `clone` on `&str` copies the reference, which does not do anything and can be removed
#10 50.84     = note: `#[warn(noop_method_call)]` on by default

[erinyoung]

The results from the test look good

#16 [test 4/4] RUN date &&     sylph sketch -i e.coli-*.fasta -o database &&     sylph sketch o157_reads.fastq  &&     sylph query database.syldb *.sylsp > ani_queries.tsv &&     sylph profile database.syldb *.sylsp > profiling.tsv &&     cat *.tsv &&     date
#16 0.053 Thu Dec  7 20:14:23 UTC 2023
#16 0.055 2023-12-07T20:14:23.855Z INFO  [sylph::sketch] Sketching genomes...
#16 0.087 2023-12-07T20:14:23.887Z INFO  [sylph::sketch] Wrote all genome sketches to database.syldb
#16 0.088 2023-12-07T20:14:23.888Z INFO  [sylph::sketch] Finished.
#16 0.091 2023-12-07T20:14:23.891Z INFO  [sylph::sketch] Sketching non-paired sequences...
#16 0.104 2023-12-07T20:14:23.904Z INFO  [sylph::sketch] Sketching ./o157_reads.fastq.sylsp complete.
#16 0.104 2023-12-07T20:14:23.905Z INFO  [sylph::sketch] Finished.
#16 0.106 2023-12-07T20:14:23.906Z INFO  [sylph::contain] Obtaining sketches...
#16 0.108 2023-12-07T20:14:23.908Z INFO  [sylph::contain] Finished obtaining genome sketches.
#16 0.122 2023-12-07T20:14:23.922Z INFO  [sylph::contain] Finished sample o157_reads.fastq.sylsp.
#16 0.122 2023-12-07T20:14:23.922Z INFO  [sylph::contain] sylph finished.
#16 0.124 2023-12-07T20:14:23.924Z INFO  [sylph::contain] Obtaining sketches...
#16 0.125 2023-12-07T20:14:23.926Z INFO  [sylph::contain] Finished obtaining genome sketches.
#16 0.143 2023-12-07T20:14:23.943Z INFO  [sylph::contain] o157_reads.fastq.sylsp taxonomic profiling; reassigning k-mers for 4 genomes...
#16 0.171 2023-12-07T20:14:23.971Z INFO  [sylph::contain] o157_reads.fastq.sylsp has 2 genomes passing profiling threshold. 
#16 0.171 2023-12-07T20:14:23.971Z INFO  [sylph::contain] Finished sample o157_reads.fastq.sylsp.
#16 0.171 2023-12-07T20:14:23.971Z INFO  [sylph::contain] sylph finished.
#16 0.173 Sample_file	Genome_file	Adjusted_ANI	Eff_cov	ANI_5-95_percentile	Eff_lambda	Lambda_5-95_percentile	Median_cov	Mean_cov_geq1	Containment_ind	Naive_ANI	Contig_name
#16 0.173 o157_reads.fastq	e.coli-o157.fasta	100.00	0.200	98.66-102.43	0.200	0.10-0.32	1	1.740	77/366	95.10	NZ_CP017439.1 Escherichia coli O157:H7 strain 2159 plasmid pO157, complete sequence
#16 0.173 o157_reads.fastq	e.coli-o157.fasta	99.74	0.361	99.61-99.94	0.361	0.34-0.38	1	1.188	6149/21556	96.03	NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
#16 0.173 o157_reads.fastq	e.coli-EC590.fasta	98.25	0.319	98.06-98.55	0.319	0.29-0.34	1	1.172	3122/19330	94.29	NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome
#16 0.173 o157_reads.fastq	e.coli-K12.fasta	98.16	0.327	97.96-98.47	0.327	0.29-0.35	1	1.171	3114/19485	94.26	NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence
#16 0.173 Sample_file	Genome_file	Taxonomic_abundance	Sequence_abundance	Adjusted_ANI	Eff_cov	ANI_5-95_percentile	Eff_lambda	Lambda_5-95_percentile	Median_cov	Mean_cov_geq1	Containment_ind	Naive_ANI	Contig_name
#16 0.173 o157_reads.fastq	e.coli-o157.fasta	64.3699	99.0626	99.74	0.361	99.61-99.94	0.361	0.34-0.38	1	1.188	6147/21556	96.03	NZ_CP017438.1 Escherichia coli O157:H7 strain 2159 chromosome, complete genome
#16 0.173 o157_reads.fastq	e.coli-o157.fasta	35.6301	0.9374	100.00	0.200	98.66-102.43	0.200	0.10-0.32	1	1.740	77/366	95.10	NZ_CP017439.1 Escherichia coli O157:H7 strain 2159 plasmid pO157, complete sequence

[erinyoung]

I think we can merge this PR, but I'd like clarity that the compilation warning can be ignored.

[stephenturner]

There is one warning during compiling. Is this something that can be ignored?

#10 50.29    Compiling sylph v0.4.1 (/sylph-0.4.1)
#10 50.84 warning: call to `.clone()` on a reference in this situation does nothing
#10 50.84    --> src/contain.rs:485:47
#10 50.84     |
#10 50.84 485 |         let file = File::open(read_sketch_file.clone()).expect(&format!(
#10 50.84     |                                               ^^^^^^^^ help: remove this redundant call
#10 50.84     |
#10 50.84     = note: the type `str` does not implement `Clone`, so calling `clone` on `&str` copies the reference, which does not do anything and can be removed
#10 50.84     = note: `#[warn(noop_method_call)]` on by default

I wish I knew the answer to this. I think the rust compiler is telling you that this .clone() isn't necessary.

[erinyoung]

It's probably fine (seems to run okay).

I'm going to

1. merge this PR
2. deploy sylph to dockerhub and quay with the tags "0.4.1" and "latest"

[erinyoung]

Thank you for your contribution!

You can check the status of the deploy here https://github.com/StaPH-B/docker-builds/actions/runs/7135566344

Let us know if you run into problems