Resource requirement and abstraction process fixes

[jfy133]

This includes a range of bug fixes and enhancements

1. Generalises default resource requirements rather than process specific settings with withLabel to address Generalise base.configs #310
2. Fixes a bug reported by Marcel Keller that genotyping was only running for one sample. This was due to the reference FASTA being consumed. I also expanded to ensure all processes have independent FASTA input channels. (thanks to @drpatelh @mahesh-panchal for troubleshooting)
3. Adds an ignore for pipe errors (exit code 141) for pmdtools as pmdtools still fails even if samtools says 'err no'
4. Adds documentation for pipeline specific institutional profiles.
5. Fixes an instability with using tee for samtools which was trying to paralellise within a paralellised process

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 necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md