Address problems pointed out by nf-core lint

Output from nf-core lint (https://nf-co.re/tools#linting-a-workflow):
% nf-core lint RUMP

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 1.12.1

INFO     Testing pipeline: RUMP                                                                                           lint.py:201
Running lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 17 » check_files_existCRITICAL Found test failures in `check_files_exist`, halting lint run.                                                    lint.py:242
╭───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 5 Test Warnings                                                                                                               │
├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ https://nf-co.re/errors#1: File not found: environment.yml                                                                        │
│ https://nf-co.re/errors#1: File not found: conf/base.config                                                                       │
│ https://nf-co.re/errors#1: File not found: .github/workflows/awstest.yml                                                          │
│ https://nf-co.re/errors#1: File not found: .github/workflows/awsfulltest.yml                                                      │
│ https://nf-co.re/errors#1: File should be removed: .travis.yml                                                                    │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [✗] 8 Tests Failed                                                                                                                │
├───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ https://nf-co.re/errors#1: File not found: nextflow_schema.json                                                                   │
│ https://nf-co.re/errors#1: File not found: CHANGELOG.md                                                                           │
│ https://nf-co.re/errors#1: File not found: docs/README.md                                                                         │
│ https://nf-co.re/errors#1: File not found: docs/output.md                                                                         │
│ https://nf-co.re/errors#1: File not found: docs/usage.md                                                                          │
│ https://nf-co.re/errors#1: File not found: .github/workflows/branch.yml                                                           │
│ https://nf-co.re/errors#1: File not found: .github/workflows/ci.yml                                                               │
│ https://nf-co.re/errors#1: File not found: .github/workflows/linting.yml                                                          │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]   9 Tests Passed  │
│ [!]   5 Test Warnings │
│ [✗]   8 Tests Failed  │
╰───────────────────────╯
lemaslab / rump

Address problems pointed out by nf-core lint #94
