All in the sample table

What's Changed

• Qc reads, assembly are now written in the sample.tsv from the start. This should fix errors of partial writing to the sample.tsv #695
• It also allows you to add external assemblies.
• singletons reads are no longer used trough the pipeline.
• This changes the default paths for raw reads and assemblies.
  assembly are now in Assembly/fasta/{sample}.fasta
  reads: QC/reads/{sample}_{fraction}.fastq.gz

Seemless update: If you update atlas and continue on an old project. Your old files will be copies. Or the path defined in the sample.tsv will be used.