Fix bugs in qc_bam and prepare_genome subworkflows and add tests

[beatrizsavinhas]

• Fix bug where the output files from picard_collectmultiplemetrics, run in subworkflow QC_BAM were not being passed to ch_multiqc_files (only the files from picard_collecthsmetrics were collected).

  seqinspector/workflows/seqinspector.nf

  Line 171 in 07e8f87

  ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)

• Fix bug in mandatory subworkflow PREPARE_GENOME where the input channel was set to an empty channel which caused the subworkflow to be skipped when running the pipeline.

  seqinspector/subworkflows/local/prepare_genome/main.nf

  Line 21 in 5793f37

  ch_reference_fasta = channel.empty()

• Add tests for subworkflow PREPARE_GENOME.

• Updated shapshots for existing pipeline tests.

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!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/seqinspector branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[MatthiasZepper]

Thank you for your contribution. I appreciate that you have added additional tests in the process and of course that bug needs to be corrected.

I suggest making the test data configurable, but this is not mandatory at this point, because I think, we will have to refactor all the tests anyway prior to a release...

[maxulysse]

Apologies for pushing commit to your branch without warning, but wanted to solve merge conflicts

[beatrizsavinhas]

Ah thanks for fixing it @maxulysse! I was awaiting a second review since I had changed some things after the first review but now that you have also approved it, I will merge the PR!