FASTQ files for external samples should not have the prefix in their names

[Nicklas Nordborg]

External samples typically have a prefix followed by and underscore and then the rest of the sample name: NN_ABC. This name is used throughout the lab processing and secondary analysis to generate names of child items and files. For example FASTQ files:

NN_ABC.m.c.lib.g.R1_fastq.gz
NN_ABC.m.c.lib.g.R2_fastq.gz

The prefix should be kept on items in BASE, but it should be skipped for file names, since the prefix also causes a top-level directory to be created:

NN/ABC/m.c.lib/ABC.m.c.lib.g.R1.fastq.gz
NN/ABC/m.c.lib/ABC.m.c.lib.g.R2.fastq.gz

[Nicklas Nordborg]

In 5524:

Fixes #1158: FASTQ files for external samples should not have the prefix in their names

Names for FASTQ files are now generated without a prefix.