[User Story] Implement nf-test

[fellen31]

Need

As a developer, I look less and less at real data produced by the pipeline. I want to be sure that a refactoring of a subworkflow doesn't affect the output files.

Suggested approach

Implement basic nf-test before a subworkflow is refactored.

Can be closed when

Modules

Subworkflows

•  Update local modules to nf-core #20
• Implement nf-test for prepare_genome
• Implement nf-test for bam_to_fastq
• Implement nf-test for bam_infer_sex
• Implement nf-test for assembly
• Implement nf-test for assembly_variant_calling
• Implement nf-test for call_paralogs
• Implement nf-test for qc_aligned_reads
• Implement nf-test for structural_variant_calling #188
• Implement nf-test for short_variant_calling #220
• Implement nf-test for cnv
• Implement nf-test for call_repeat_expansions #414
• Implement nf-test for annotate_repeat_expansions #415
• Implement nf-test for methylation
• Implement nf-test for phasing #273
• Implement nf-test for snv_annotation #242
• Implement nf-test for rank_variants #283
• Rename and add nf-test to structural variant calling #346

Workflows

• Implement nf-test for NALLO #218