Fixes #18: "schema_input.json" does not accept uncompressed contigs

[sgsutcliffe]

The input file for running staramrnf had a restrictive pattern for contigs column in the schema_input.json such that only compressed files with .gz file extension could be included. To allow for uncompressed files I modified the regex pattern.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.

[sgsutcliffe]

To test the change I ran the nextflow run . -profile test,docker --outdir results --input samplesheet.csv using uncompressed versions of the test/genomes with extensions .fna, .fasta and .fa using a modified samplesheet.csv

sample,contigs,species
GCA_000008105,tests/genomes/salmonella/GCA_000008105.1_ASM810v1_genomic.fasta,Salmonella
GCA_000947975,tests/genomes/ecoli/GCA_000947975.1_ASM94797v1_genomic.fa,Escherichia coli
GCF_000196035,tests/genomes/listeria/GCF_000196035.1_ASM19603v1_genomic.fna,Listeria monocytogenes

[sgsutcliffe]

I will include one of the uncompressed genomes to use as test for nf-test for CI

[sgsutcliffe]

The genome file paths in the tests/assets/test_samplesheet.csv and assets/samplesheet.csv used by nf-test and nextflow run phac-nml/staramrnf -profile docker,test, respectively, point to genomes via URLs on dev branch. I updated the files to uncompressed versions on the dev branch. See commits to dev to allow for CI to pass for this PR 52a476a 05b4a3c df69014

[kylacochrane]

This looks great Steven 😄

[kylacochrane]

I don't think you need to include this uncompressed fasta file anymore since it's already been pushed to the dev branch. However, it shouldn't cause any issues, and keeping it might actually make merging easier, as the branches will align more closely... up to you 😆

[sgsutcliffe]

I'd made the commit prior to including the uncompressed genome on dev and just decided to do less work i.e. roll back the commit, but it does appear like redundant work 😆

[apetkau]

As long as it all works (e.g., no merge conflicts when merging back into dev) then you can leave as-is.

[apetkau]

This looks great Steven. Thanks so much. Just one small change on the error message being printed out (given in-line below).

[apetkau]

As long as it all works (e.g., no merge conflicts when merging back into dev) then you can leave as-is.

[apetkau]

Everything looks great to me. Thanks so much 😄

[emarinier]

Looks good to me. Thanks Steven.