Prepare version 3 release for Nanopore analysis

[peterk87]

This PR is to prepare a v3 release of the workflow adding a Nanopore analysis subworkflow.

The workflow's name has been changed from nf-iav-illumina to nf-flu and the official repo for nf-flu will be CFIA-NCFAD/nf-flu going forward.

• Added back bin/fastq_dir_to_samplesheet.py for Illumina --input samplesheet creation from Illumina FASTQ reads directory
• Fixed issue #12. Nanopore sample sheet can specify a mix of single FASTQ files and/or directories containing FASTQ files. Different reads with the same sample name will be merged prior to analysis. FASTQs can be GZIP compressed and have the extensions: .fastq, .fq, .fastq.gz, .fq.gz. Updated CI tests to test for this flexible sample sheet handling.
• Switched to GitHub YAML form for bug report template from Markdown template.
• CI tests now output results/pipeline_info/ and .nextflow.log as artifacts for easier debugging of issues.

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] Ensure the test suite passes (nextflow run . -profile test,docker).
• [X] Usage Documentation in docs/usage.md is updated.
• [X] Output Documentation in docs/output.md is updated.
• [X] CHANGELOG.md is updated.
• [X] README.md is updated (including new tool citations and authors/contributors).

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[nhhaidee]

@peterk87 I found some bugs from initial test

• Tag of process VCF_FILTER_FRAMESHIFT display incorrectly NF_FLU:NANOPORE:VCF_FILTER_FRAMESHIFT (ERR6359502|5_NP|null). It is caused by https://github.com/peterk87/nf-flu/blob/d94de883b22956a92dc066598e11a4a275633bd3/modules/local/vcf_filter_frameshift.nf#L2 It should be $ref_id
• In publish_dir/variants and publish_dir/reference_sequences, there is a strange folder name [:]
• In MultiQC Report, there is sample name ERR6359501.Segment_1_PB2.MH201221.no_frameshifts

[peterk87]

@peterk87 I found some bugs from initial test

* Tag of process  `VCF_FILTER_FRAMESHIFT` display incorrectly `NF_FLU:NANOPORE:VCF_FILTER_FRAMESHIFT (ERR6359502|5_NP|null)`. It is caused by  https://github.com/peterk87/nf-flu/blob/d94de883b22956a92dc066598e11a4a275633bd3/modules/local/vcf_filter_frameshift.nf#L2

  It should be `$ref_id`

* In `publish_dir/variants` and `publish_dir/reference_sequences`, there is a strange folder name `[:]`

* In MultiQC Report, there is sample name `ERR6359501.Segment_1_PB2.MH201221.no_frameshifts`

Thanks @nhhaidee ! All of these should be fixed in 19698ba

[nhhaidee]

@peterk87 The changes look very good to me and tests passed at my end as well, I think you can release it

[peterk87]

Thanks @nhhaidee ! I've made a new release at https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.1.0