New output directory structure

[nvnieuwk]

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
• Make sure your code lints (nf-core 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).

[nvnieuwk]

Don't merge before #213 has been merged

[nvnieuwk]

The new output directory now looks like this (for the test profile):

results/
├── Proband_12345
│   ├── NA24143_v1_9_0dev_2024_11_07
│   │   ├── NA24143.bed
│   │   ├── NA24143.haplotypecaller.bcftools_stats.txt
│   │   ├── NA24143.haplotypecaller.g.vcf.gz
│   │   └── NA24143.haplotypecaller.g.vcf.gz.tbi
│   ├── NA24149_v1_9_0dev_2024_11_07
│   │   ├── NA24149.bed
│   │   ├── NA24149.haplotypecaller.bcftools_stats.txt
│   │   ├── NA24149.haplotypecaller.g.vcf.gz
│   │   └── NA24149.haplotypecaller.g.vcf.gz.tbi
│   ├── NA24385_v1_9_0dev_2024_11_07
│   │   ├── NA24385.bed
│   │   ├── NA24385.haplotypecaller.bcftools_stats.txt
│   │   ├── NA24385.haplotypecaller.g.vcf.gz
│   │   └── NA24385.haplotypecaller.g.vcf.gz.tbi
│   ├── output_v1_9_0dev_2024_11_07
│   │   ├── automap
│   │   │   └── haplotypecaller
│   │   │       ├── sample1
│   │   │       │   ├── sample1.HomRegions.cmgg_bio.tsv
│   │   │       │   ├── sample1.HomRegions.pdf
│   │   │       │   ├── sample1.HomRegions.strict.cmgg_bio.tsv
│   │   │       │   └── sample1.HomRegions.tsv
│   │   │       ├── sample2
│   │   │       │   ├── sample2.HomRegions.cmgg_bio.tsv
│   │   │       │   ├── sample2.HomRegions.pdf
│   │   │       │   ├── sample2.HomRegions.strict.cmgg_bio.tsv
│   │   │       │   └── sample2.HomRegions.tsv
│   │   │       └── sample3
│   │   │           ├── sample3.HomRegions.cmgg_bio.tsv
│   │   │           ├── sample3.HomRegions.pdf
│   │   │           ├── sample3.HomRegions.strict.cmgg_bio.tsv
│   │   │           └── sample3.HomRegions.tsv
│   │   ├── Proband_12345.haplotypecaller.bed
│   │   ├── Proband_12345.haplotypecaller.db
│   │   ├── Proband_12345.haplotypecaller.ped
│   │   ├── Proband_12345.haplotypecaller.vcf.gz
│   │   └── Proband_12345.haplotypecaller.vcf.gz.tbi
│   └── qc_v1_9_0dev_2024_11_07
│       ├── Proband_12345.haplotypecaller.bcftools_stats.txt
│       └── Proband_12345.haplotypecaller.html
└── v1_9_0dev_2024_11_07
    ├── execution_report_2024-11-07_17-33-49.html
    ├── execution_timeline_2024-11-07_17-33-49.html
    ├── execution_trace_2024-11-07_17-33-49.html
    ├── multiqc_report.html
    ├── params_2024-11-07_17-34-02.json
    ├── pipeline_dag_2024-11-07_17-33-49.html
    ├── pipeline_software_mqc_versions.yml
    └── samplesheet.csv