Pipeline update

[zb32]

PR checklist

• [X] This comment contains a description of changes (with reason). Implements new SAMTOOLS/VIEW module from NF-CORE as MOSDEPTH requires a index file
• [ ] 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 Link not working
  • [ ] If necessary, also make a PR on the nf-core/blobtoolkit branch on the nf-core/test-datasets repository.
• [x] Make sure your code lints (nf-core lint).
• [X] Ensure the test suite passes (nextflow run . -profile 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).

[zb32]

• Make requested changes to pipeline.
• Test test.config locally with .sandbox.
• Update test.config to work with s3
• Test updated test.config
• Make sure all tests pass in GitHub, if not list why in your PR. Sometimes nf-core linting fails because we have modified the original template, but the failures must be within reason.

All requested changes made and test.config updated to work with S3. All tests passed apart from nf-core linting which fails because a python module is not found.

[priyanka-surana]

Regarding the modules folder, make sure the structure matches the repo nf-core/modules. If not delete and re-install. Also delete the modules config from your home dir and the modules json file from your pipeline directory.

Alternatively, if the pipeline runs without errors (which it seems to), move on to the other 2 modules (fasta_windows and mosdepth) and we can fix the linting errors and merge later.