Add sylph/profile module

[sofstam]

PR checklist

Moves the local module sylph/profile to nf-core modules. Closes nf-core/seqinspector#65
Removes unnecessary pattern from sylph/sketch meta file.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

Suggested to be a bit more specific about the created csv :)

[famosab]

Is it expected that the contains check always leads to the string not being contained?

[sofstam]

The string should be contained. Looking into it.

[famosab]

MAybe you can assert the file a bit better using: https://github.com/lukfor/nft-csv

[sofstam]

Do you mean to count the columns of the output file?

[famosab]

anything that makes sense - counting columns or asserting column header both seems fine to me

[sofstam]

Updated this now.

[SPPearce]

@sofstam , do you need a hand to get this finished off?

[sofstam]

@SPPearce Was on holidays, looking at the comments now :)

[SPPearce]

Can probably just do this. You don't need to name the snapshots if you only have one per test.

Suggested change

	{ assert snapshot(process.out.versions).match("versions_single") },
	{ assert output_content.size() > 1 }, // Ensure there's at least a header and one data line
	{ assert output_content[0] == "Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name" },
	{ assert snapshot(output_content.take(5).join("\n")).match("profile_out_content_single") } // Snapshot first 5 lines
	{ assert snapshot(
	process.out.versions,
	output_content.take(5).join("\n")
	).match() },
	{ assert output_content.size() > 1 }, // Ensure there's at least a header and one data line
	{ assert output_content[0] == "Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name" }

Or you could probably do:

Suggested change

	{ assert snapshot(process.out.versions).match("versions_single") },
	{ assert output_content.size() > 1 }, // Ensure there's at least a header and one data line
	{ assert output_content[0] == "Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name" },
	{ assert snapshot(output_content.take(5).join("\n")).match("profile_out_content_single") } // Snapshot first 5 lines
	{ assert snapshot(
	process.out.versions,
	file(output_content).readLines()[0..4]
	).match() }

[SPPearce]

One of my comments may have been related to some previous code, can't see the comment on my phone

[mahesh-panchal]

Is there not a specific file or contents to test for here?

[mahesh-panchal]

Could you update this test so there's a specific file to test please?

[famosab]

Just some questions about the assertions. Looks good to me otherwise :)

[famosab]

Suggested change

	{ assert snapshot(process.out).match("stub_output") }
	{ assert snapshot(process.out).match() }

[famosab]

Is there a way to bring this assertion into the snapshot? Can we maybe assert the headers of the tsv or something similar?

[famosab]

Maybe like @SPPearce suggested:

                { assert snapshot(
                    process.out.versions,
                    file(output_content).readLines()[0..4]
                    ).match() }

[famosab]

Suggested change

	e.g. [ id:'test', single_end:false ]
	e.g. [ id:'test']