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

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] Make sure your code lints (nf-core lint).
• [x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [x] 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 52a476a664eb3e5556af724bfd85a52d703dce62 05b4a3c0d440494c19fcd3ecb462b825c2d0a88c df6901438e31f00a86621da10ee1a27a928926c3