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Use authentication for GitHub API calls in linting #1496

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2 tasks
ewels opened this issue Mar 25, 2022 · 0 comments
Closed
2 tasks

Use authentication for GitHub API calls in linting #1496

ewels opened this issue Mar 25, 2022 · 0 comments
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@ewels
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automation command line tools Anything to do with the cli interfaces high-priority
Milestone
2.4

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@ewels
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ewels commented Mar 25, 2022

Description of feature

As pipelines move to DSL2 with more modules, the nf-core lint command that runs in CI is starting to do a lot of API calls to check that modules are unchanged.

We're starting to see some fail due to 403 errors, which I guess are us hitting the unauthenticated rate limit.

  • Catch all API exceptions and log the full response (as we do for nf-core sync)
  • Authenticate if we can, if the GITHUB_TOKEN env var is set (see GH docs example)
Failing actions log 
,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.3.2 - https://nf-co.re


INFO     Testing pipeline: /home/runner/work/sarek/sarek         __init__.py:243


╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/bin/nf-core:8 in <module>             │
│                                                                              │
│   7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])     │
│ ❱ 8 │   sys.exit(run_nf_core())                                              │
│   9                                                                          │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/_ │
│ _main__.py:90 in run_nf_core                                                 │
│                                                                              │
│    89 │   # Lanch the click cli                                              │
│ ❱  90 │   nf_core_cli()                                                      │
│    91                                                                        │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/click/cor │
│ e.py:[11](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:11)28 in __call__                                                        │
│                                                                              │
│   1[12](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:12)7 │   │   """Alias for :meth:`main`."""                                 │
│ ❱ 1128 │   │   return self.main(*args, **kwargs)                             │
│   1129                                                                       │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/rich_clic │
│ k/rich_click.py:594 in main                                                  │
│                                                                              │
│   593 │   │   try:                                                           │
│ ❱ 594 │   │   │   return super().main(*args, standalone_mode=False, **kwargs │
│   595 │   │   except click.ClickException as e:                              │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/click/cor │
│ e.py:1053 in main                                                            │
│                                                                              │
│   1052 │   │   │   │   with self.make_context(prog_name, args, **extra) as c │
│ ❱ 1053 │   │   │   │   │   rv = self.invoke(ctx)                             │
│   1054 │   │   │   │   │   if not standalone_mode:                           │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/click/cor │
│ e.py:1659 in invoke                                                          │
│                                                                              │
│   1658 │   │   │   │   with sub_ctx:                                         │
│ ❱ 1659 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub │
│   1660                                                                       │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/click/cor │
│ e.py:[13](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:13)95 in invoke                                                          │
│                                                                              │
│   1394 │   │   if self.callback is not None:                                 │
│ ❱ 1395 │   │   │   return ctx.invoke(self.callback, **ctx.params)            │
│   1396                                                                       │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.[15](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:15)/x64/lib/python3.6/site-packages/click/cor │
│ e.py:754 in invoke                                                           │
│                                                                              │
│    753 │   │   │   with ctx:                                                 │
│ ❱  754 │   │   │   │   return __callback(*args, **kwargs)                    │
│    755                                                                       │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/_ │
│ _main__.py:328 in lint                                                       │
│                                                                              │
│   3[27](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:27) │   │   lint_obj, module_lint_obj = nf_core.lint.run_linting(          │
│ ❱ 3[28](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:28) │   │   │   dir, release, fix, key, show_passed, fail_ignored, markdow │
│   3[29](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:29) │   │   )                                                              │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/l │
│ int/__init__.py:102 in run_linting                                           │
│                                                                              │
│   101 │   if len(module_lint_obj.all_nfcore_modules) > 0:                    │
│ ❱ 102 │   │   module_lint_obj.lint_modules(module_lint_obj.all_nfcore_module │
│   103                                                                        │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/m │
│ odules/lint/__init__.py:[30](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:30)6 in lint_modules                                  │
│                                                                              │
│   305 │   │   │   │   progress_bar.update(lint_progress, advance=1, test_nam │
│ ❱ 306 │   │   │   │   self.lint_module(mod, local=local)                     │
│   307                                                                        │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/m │
│ odules/lint/__init__.py:[33](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:33)4 in lint_module                                   │
│                                                                              │
│   333 │   │   │   for test_name in self.lint_tests:                          │
│ ❱ 3[34](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:34) │   │   │   │   getattr(self, test_name)(mod)                          │
│   3[35](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:35)                                                                        │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/nf_core/m │
│ odules/lint/module_version.py:41 in module_version                           │
│                                                                              │
│   [40](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:40) │   │   try:                                                            │
│ ❱ [41](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:41) │   │   │   module_git_log =                                            │
│      nf_core.modules.module_utils.get_module_git_log(module.module_name)     │
│   [42](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:42) │   │   │   if git_sha == module_git_log[0]["git_sha"]:                 │
│                                                                              │
│ /opt/hostedtoolcache/Python/3.6.15/x[64](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:64)/lib/python3.6/site-packages/nf_core/m │
│ odules/module_utils.py:84 in get_module_git_log                              │
│                                                                              │
│    [83](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:83) │   │   raise LookupError(                                             │
│ ❱  [84](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:84) │   │   │   f"Unable to fetch commit SHA for module {module_name}. API │
│       '{response.status_code}'"                                              │
│    [85](https://github.com/nf-core/sarek/runs/5689044442?check_suite_focus=true#step:6:85) │   │   )                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
LookupError: Unable to fetch commit SHA for module tabix/tabix. API responded 
with '403'
Error: Process completed with exit code 1.
Cleaned up verbose log 
[2022-03-25 08:33:21,575] git.cmd              [DEBUG  ]  Popen(['git', 'cat-file', '--batch-check'], cwd=/home/runner/work/sarek/sarek, universal_newlines=False, shell=None, istream=<valid stream>)
[2022-03-25 08:33:21,581] nf_core.utils        [DEBUG  ]  Got '/home/runner/work/sarek/sarek' as path
[2022-03-25 08:33:21,581] nf_core.utils        [DEBUG  ]  No config cache found
[2022-03-25 08:33:25,455] nf_core.utils        [DEBUG  ]  Saving config cache: /home/runner/.nextflow/nf-core/wf-config-cache-da664ede42120a3d40f8bbf23.json
[2022-03-25 08:33:25,652] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/branches HTTP/1.1" 200 1345
[2022-03-25 08:33:25,843] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/contents?ref=master HTTP/1.1" 200 1494
[2022-03-25 08:33:25,850] nf_core.modules.modules_command [DEBUG  ]  No lint config file found: /home/runner/work/sarek/sarek/.nf-core-lint.yaml
[2022-03-25 08:33:25,851] nf_core.lint         [INFO   ]  Testing pipeline: [magenta]/home/runner/work/sarek/sarek
[2022-03-25 08:33:25,854] nf_core.lint         [DEBUG  ]  Running lint test: files_exist
[2022-03-25 08:33:25,855] nf_core.lint         [DEBUG  ]  Running lint test: nextflow_config
[2022-03-25 08:33:25,856] nf_core.lint         [DEBUG  ]  Running lint test: files_unchanged
[2022-03-25 08:33:25,971] urllib3.connectionpool [DEBUG  ]  Starting new HTTPS connection (1): nf-co.re:443
[2022-03-25 08:33:26,570] urllib3.connectionpool [DEBUG  ]  https://nf-co.re:443 "GET /logo/sarek?theme=light&w=400 HTTP/1.1" 200 None
[2022-03-25 08:33:26,580] urllib3.connectionpool [DEBUG  ]  Starting new HTTPS connection (1): nf-co.re:443
[2022-03-25 08:33:27,259] urllib3.connectionpool [DEBUG  ]  https://nf-co.re:443 "GET /logo/sarek?theme=light?w=600&theme=dark HTTP/1.1" 200 None
[2022-03-25 08:33:27,490] urllib3.connectionpool [DEBUG  ]  Starting new HTTPS connection (1): nf-co.re:443
[2022-03-25 08:33:27,984] urllib3.connectionpool [DEBUG  ]  https://nf-co.re:443 "GET /logo/sarek?theme=light?w=600&theme=light HTTP/1.1" 200 None
[2022-03-25 08:33:28,221] git.cmd              [DEBUG  ]  Popen(['git', 'init'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=None)
[2022-03-25 08:33:28,230] git.cmd              [DEBUG  ]  Popen(['git', 'add', '-A'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=None)
[2022-03-25 08:33:28,355] git.cmd              [DEBUG  ]  Popen(['git', 'cat-file', '--batch-check'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=<valid stream>)
[2022-03-25 08:33:28,361] git.cmd              [DEBUG  ]  Popen(['git', 'cat-file', '--batch'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=<valid stream>)
[2022-03-25 08:33:28,366] git.cmd              [DEBUG  ]  Popen(['git', 'branch', 'TEMPLATE'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=None)
[2022-03-25 08:33:28,371] git.cmd              [DEBUG  ]  Popen(['git', 'branch', 'dev'], cwd=/tmp/tmp_tpvkteu/nf-core-sarek, universal_newlines=False, shell=None, istream=None)
[2022-03-25 08:33:28,387] nf_core.lint         [DEBUG  ]  Running lint test: actions_ci
[2022-03-25 08:33:28,399] nf_core.lint         [DEBUG  ]  Running lint test: actions_awstest
[2022-03-25 08:33:28,402] nf_core.lint         [DEBUG  ]  Running lint test: actions_awsfulltest
[2022-03-25 08:33:28,407] nf_core.lint         [DEBUG  ]  Running lint test: readme
[2022-03-25 08:33:28,407] nf_core.lint         [DEBUG  ]  Running lint test: pipeline_todos
[2022-03-25 08:33:28,922] nf_core.lint         [DEBUG  ]  Running lint test: pipeline_name_conventions
[2022-03-25 08:33:28,922] nf_core.lint         [DEBUG  ]  Running lint test: template_strings
[2022-03-25 08:33:29,026] nf_core.lint         [DEBUG  ]  Running lint test: schema_lint
[2022-03-25 08:33:29,041] nf_core.utils        [DEBUG  ]  Got '/home/runner/work/sarek/sarek' as path
[2022-03-25 08:33:29,041] nf_core.utils        [DEBUG  ]  Found a config cache, loading: /home/runner/.nextflow/nf-core/wf-config-cache-da664ede42120a3d40f8bbf23.json
[2022-03-25 08:33:29,042] nf_core.lint         [DEBUG  ]  Running lint test: schema_params
[2022-03-25 08:33:29,042] nf_core.utils        [DEBUG  ]  Got '/home/runner/work/sarek/sarek' as path
[2022-03-25 08:33:29,042] nf_core.utils        [DEBUG  ]  Found a config cache, loading: /home/runner/.nextflow/nf-core/wf-config-cache-da664ede42120a3d40f8bbf23.json
[2022-03-25 08:33:29,055] nf_core.lint         [DEBUG  ]  Running lint test: schema_description
[2022-03-25 08:33:29,055] nf_core.utils        [DEBUG  ]  Got '/home/runner/work/sarek/sarek' as path
[2022-03-25 08:33:29,056] nf_core.utils        [DEBUG  ]  Found a config cache, loading: /home/runner/.nextflow/nf-core/wf-config-cache-da664ede42120a3d40f8bbf23.json
[2022-03-25 08:33:29,067] nf_core.lint         [DEBUG  ]  Running lint test: actions_schema_validation
[2022-03-25 08:33:29,072] urllib3.connectionpool [DEBUG  ]  Starting new HTTPS connection (1): json.schemastore.org:443
[2022-03-25 08:33:29,543] urllib3.connectionpool [DEBUG  ]  https://json.schemastore.org:443 "GET /github-workflow HTTP/1.1" 200 13252
[2022-03-25 08:33:29,691] nf_core.lint         [DEBUG  ]  Running lint test: merge_markers
[2022-03-25 08:33:30,196] nf_core.lint         [DEBUG  ]  Running lint test: modules_json
[2022-03-25 08:33:30,397] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/contents HTTP/1.1" 200 1494
[2022-03-25 08:33:30,406] nf_core.lint         [DEBUG  ]  Running lint test: multiqc_config
[2022-03-25 08:33:30,418] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'ascat' from github API
[2022-03-25 08:33:30,652] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/ascat&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 4596
[2022-03-25 08:33:30,811] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/ascat/main.nf HTTP/1.1" 200 2002
[2022-03-25 08:33:30,953] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/ascat/meta.yml HTTP/1.1" 200 1113
[2022-03-25 08:33:30,964] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'bcftools/stats' from github API
[2022-03-25 08:33:31,234] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/bcftools/stats&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:31,408] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bcftools/stats/main.nf HTTP/1.1" 200 515
[2022-03-25 08:33:31,599] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bcftools/stats/meta.yml HTTP/1.1" 200 496
[2022-03-25 08:33:31,611] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'bwa/index' from github API
[2022-03-25 08:33:31,909] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/bwa/index&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:32,124] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bwa/index/main.nf HTTP/1.1" 200 488
[2022-03-25 08:33:32,272] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bwa/index/meta.yml HTTP/1.1" 200 423
[2022-03-25 08:33:32,283] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'bwa/mem' from github API
[2022-03-25 08:33:32,546] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/bwa/mem&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:32,752] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/bwa/mem/main.nf HTTP/1.1" 200 746
[2022-03-25 08:33:32,906] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/bwa/mem/meta.yml HTTP/1.1" 200 644
[2022-03-25 08:33:32,919] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'bwamem2/index' from github API
[2022-03-25 08:33:33,153] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/bwamem2/index&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:33,313] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bwamem2/index/main.nf HTTP/1.1" 200 474
[2022-03-25 08:33:33,462] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/bwamem2/index/meta.yml HTTP/1.1" 200 386
[2022-03-25 08:33:33,473] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'bwamem2/mem' from github API
[2022-03-25 08:33:33,719] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/bwamem2/mem&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:33,912] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/bwamem2/mem/main.nf HTTP/1.1" 200 739
[2022-03-25 08:33:34,061] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/bwamem2/mem/meta.yml HTTP/1.1" 200 639
[2022-03-25 08:33:34,073] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'cat/fastq' from github API
[2022-03-25 08:33:34,342] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/cat/fastq&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 11580
[2022-03-25 08:33:34,496] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/cat/fastq/main.nf HTTP/1.1" 200 673
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[2022-03-25 08:33:35,293] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'controlfreec' from github API
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[2022-03-25 08:33:35,826] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'custom/dumpsoftwareversions' from github API
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[2022-03-25 08:33:36,389] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'deeptools/bamcoverage' from github API
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[2022-03-25 08:33:36,974] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'deepvariant' from github API
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[2022-03-25 08:33:37,535] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'ensemblvep' from github API
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[2022-03-25 08:33:38,140] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'fastqc' from github API
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[2022-03-25 08:33:38,734] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'fgbio/callmolecularconsensusreads' from github API
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[2022-03-25 08:33:39,295] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'fgbio/fastqtobam' from github API
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[2022-03-25 08:33:39,854] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'fgbio/groupreadsbyumi' from github API
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[2022-03-25 08:33:40,396] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'freebayes' from github API
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[2022-03-25 08:33:40,985] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/genotypegvcfs' from github API
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[2022-03-25 08:33:41,628] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/haplotypecaller' from github API
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[2022-03-25 08:33:42,653] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/applybqsr' from github API
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[2022-03-25 08:33:43,288] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/learnreadorientationmodel' from github API
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[2022-03-25 08:33:43,823] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/markduplicates' from github API
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[2022-03-25 08:33:44,609] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/intervallisttobed' from github API
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[2022-03-25 08:33:45,142] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/gatherbqsrreports' from github API
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[2022-03-25 08:33:45,794] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/createsequencedictionary' from github API
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[2022-03-25 08:33:46,532] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/filtermutectcalls' from github API
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[2022-03-25 08:33:47,125] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/estimatelibrarycomplexity' from github API
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[2022-03-25 08:33:47,786] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/getpileupsummaries' from github API
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[2022-03-25 08:33:48,424] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/gatk4/getpileupsummaries/main.nf HTTP/1.1" 200 785
[2022-03-25 08:33:48,596] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/gatk4/getpileupsummaries/meta.yml HTTP/1.1" 200 984
[2022-03-25 08:33:48,609] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/gatherpileupsummaries' from github API
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[2022-03-25 08:33:49,171] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/variantrecalibrator' from github API
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[2022-03-25 08:33:49,728] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/mergemutectstats' from github API
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[2022-03-25 08:33:50,394] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/calculatecontamination' from github API
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[2022-03-25 08:33:50,936] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/baserecalibrator' from github API
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[2022-03-25 08:33:51,365] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/gatk4/baserecalibrator/main.nf HTTP/1.1" 200 790
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[2022-03-25 08:33:51,547] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/applyvqsr' from github API
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[2022-03-25 08:33:52,126] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/gatk4/applyvqsr/meta.yml HTTP/1.1" 200 975
[2022-03-25 08:33:52,138] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/genomicsdbimport' from github API
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[2022-03-25 08:33:52,566] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/967fb22dedc2c8855f00e64c3d7b5814c85242a6/modules/gatk4/genomicsdbimport/main.nf HTTP/1.1" 200 1042
[2022-03-25 08:33:52,825] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/967fb22dedc2c8855f00e64c3d7b5814c85242a6/modules/gatk4/genomicsdbimport/meta.yml HTTP/1.1" 200 1224
[2022-03-25 08:33:52,836] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'gatk4/mutect2' from github API
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[2022-03-25 08:33:53,419] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/gatk4/mutect2/main.nf HTTP/1.1" 200 995
[2022-03-25 08:33:53,570] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/gatk4/mutect2/meta.yml HTTP/1.1" 200 1192
[2022-03-25 08:33:53,583] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'manta/somatic' from github API
[2022-03-25 08:33:53,813] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/manta/somatic&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:53,969] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/somatic/main.nf HTTP/1.1" 200 817
[2022-03-25 08:33:54,121] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/somatic/meta.yml HTTP/1.1" 200 789
[2022-03-25 08:33:54,134] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'manta/germline' from github API
[2022-03-25 08:33:54,404] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/manta/germline&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:54,559] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/germline/main.nf HTTP/1.1" 200 828
[2022-03-25 08:33:54,727] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/germline/meta.yml HTTP/1.1" 200 795
[2022-03-25 08:33:54,739] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'manta/tumoronly' from github API
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[2022-03-25 08:33:55,155] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/tumoronly/main.nf HTTP/1.1" 200 758
[2022-03-25 08:33:55,316] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/979e57b7ac6a405a395dd7a6dbe1a275c5bc226b/modules/manta/tumoronly/meta.yml HTTP/1.1" 200 758
[2022-03-25 08:33:55,328] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'msisensorpro/msi_somatic' from github API
[2022-03-25 08:33:55,580] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/msisensorpro/msi_somatic&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 2556
[2022-03-25 08:33:55,732] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/msisensorpro/msi_somatic/main.nf HTTP/1.1" 200 675
[2022-03-25 08:33:55,892] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/msisensorpro/msi_somatic/meta.yml HTTP/1.1" 200 788
[2022-03-25 08:33:55,904] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'msisensorpro/scan' from github API
[2022-03-25 08:33:56,113] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/msisensorpro/scan&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 2556
[2022-03-25 08:33:56,275] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/msisensorpro/scan/main.nf HTTP/1.1" 200 527
[2022-03-25 08:33:56,439] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/f0800157544a82ae222931764483331a81812012/modules/msisensorpro/scan/meta.yml HTTP/1.1" 200 561
[2022-03-25 08:33:56,451] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'multiqc' from github API
[2022-03-25 08:33:56,744] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/multiqc&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:56,894] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/multiqc/main.nf HTTP/1.1" 200 469
[2022-03-25 08:33:57,041] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/multiqc/meta.yml HTTP/1.1" 200 525
[2022-03-25 08:33:57,052] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'qualimap/bamqc' from github API
[2022-03-25 08:33:57,305] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/qualimap/bamqc&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:57,466] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e31f1ff3b1375b30db08637d8937e25cc046f3cc/modules/qualimap/bamqc/main.nf HTTP/1.1" 200 771
[2022-03-25 08:33:57,609] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e31f1ff3b1375b30db08637d8937e25cc046f3cc/modules/qualimap/bamqc/meta.yml HTTP/1.1" 200 585
[2022-03-25 08:33:57,622] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'qualimap/bamqccram' from github API
[2022-03-25 08:33:57,868] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/qualimap/bamqccram&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 2180
[2022-03-25 08:33:58,020] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/qualimap/bamqccram/main.nf HTTP/1.1" 200 940
[2022-03-25 08:33:58,208] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/950700bcdc0e9a2b6883d40d2c51c6fc435cd714/modules/qualimap/bamqccram/meta.yml HTTP/1.1" 200 629
[2022-03-25 08:33:58,220] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samblaster' from github API
[2022-03-25 08:33:58,485] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samblaster&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:58,654] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/samblaster/main.nf HTTP/1.1" 200 703
[2022-03-25 08:33:58,809] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/samblaster/meta.yml HTTP/1.1" 200 751
[2022-03-25 08:33:58,821] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/stats' from github API
[2022-03-25 08:33:59,065] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/stats&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 13731
[2022-03-25 08:33:59,261] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/stats/main.nf HTTP/1.1" 200 544
[2022-03-25 08:33:59,421] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/stats/meta.yml HTTP/1.1" 200 633
[2022-03-25 08:33:59,434] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/index' from github API
[2022-03-25 08:33:59,718] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/index&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:33:59,907] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/index/main.nf HTTP/1.1" 200 528
[2022-03-25 08:34:00,070] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/index/meta.yml HTTP/1.1" 200 556
[2022-03-25 08:34:00,082] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/faidx' from github API
[2022-03-25 08:34:00,333] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/faidx&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:00,533] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/faidx/main.nf HTTP/1.1" 200 485
[2022-03-25 08:34:00,703] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/faidx/meta.yml HTTP/1.1" 200 519
[2022-03-25 08:34:00,716] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/mpileup' from github API
[2022-03-25 08:34:00,971] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/mpileup&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:01,204] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/mpileup/main.nf HTTP/1.1" 200 537
[2022-03-25 08:34:01,375] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/mpileup/meta.yml HTTP/1.1" 200 551
[2022-03-25 08:34:01,386] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/view' from github API
[2022-03-25 08:34:01,630] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/view&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:01,827] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/view/main.nf HTTP/1.1" 200 687
[2022-03-25 08:34:02,036] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/view/meta.yml HTTP/1.1" 200 612
[2022-03-25 08:34:02,048] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/merge' from github API
[2022-03-25 08:34:02,341] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/merge&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:02,528] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/merge/main.nf HTTP/1.1" 200 622
[2022-03-25 08:34:02,705] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/merge/meta.yml HTTP/1.1" 200 600
[2022-03-25 08:34:02,717] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'samtools/bam2fq' from github API
[2022-03-25 08:34:02,950] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/samtools/bam2fq&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:03,114] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/bam2fq/main.nf HTTP/1.1" 200 611
[2022-03-25 08:34:03,278] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/1ad73f1b2abdea9398680d6d20014838135c9a35/modules/samtools/bam2fq/meta.yml HTTP/1.1" 200 694
[2022-03-25 08:34:03,290] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'seqkit/split2' from github API
[2022-03-25 08:34:03,546] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/seqkit/split2&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:03,697] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/seqkit/split2/main.nf HTTP/1.1" 200 582
[2022-03-25 08:34:03,842] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/seqkit/split2/meta.yml HTTP/1.1" 200 463
[2022-03-25 08:34:03,855] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'snpeff' from github API
[2022-03-25 08:34:04,081] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/snpeff&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:04,296] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/snpeff/main.nf HTTP/1.1" 200 698
[2022-03-25 08:34:04,447] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/snpeff/meta.yml HTTP/1.1" 200 594
[2022-03-25 08:34:04,459] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'strelka/somatic' from github API
[2022-03-25 08:34:04,724] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/strelka/somatic&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:05,005] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/strelka/somatic/main.nf HTTP/1.1" 200 789
[2022-03-25 08:34:05,197] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/strelka/somatic/meta.yml HTTP/1.1" 200 753
[2022-03-25 08:34:05,208] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'strelka/germline' from github API
[2022-03-25 08:34:05,481] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/strelka/germline&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 200 None
[2022-03-25 08:34:05,669] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/strelka/germline/main.nf HTTP/1.1" 200 699
[2022-03-25 08:34:05,851] urllib3.connectionpool [DEBUG  ]  https://raw.githubusercontent.com:443 "GET /nf-core/modules/e745e167c1020928ef20ea1397b6b4d230681b4d/modules/strelka/germline/meta.yml HTTP/1.1" 200 630
[2022-03-25 08:34:05,863] nf_core.modules.module_utils [DEBUG  ]  Fetching commit history of module 'tabix/tabix' from github API
[2022-03-25 08:34:06,004] urllib3.connectionpool [DEBUG  ]  https://api.github.com:443 "GET /repos/nf-core/modules/commits?sha=master&path=modules/tabix/tabix&page=1&since=2021-07-07T00:00:00Z HTTP/1.1" 403 280
[2022-03-25 08:34:06,005] requests_cache.session [DEBUG  ]  Skipping cache write for URL: https://api.github.com/repos/nf-core/modules/commits?sha=master&path=modules/tabix/tabix&page=1&since=2021-07-07T00:00:00Z
@ewels ewels added automation command line tools Anything to do with the cli interfaces high-priority labels Mar 25, 2022
@ewels ewels self-assigned this Mar 25, 2022
ewels added a commit to ewels/nf-core-tools that referenced this issue Mar 29, 2022
@ewels
First stab at writing a central utils function for GitHub API calls.
91b1984 
Uses authentication from local gh CLI or a supplied bearer token if found.

Done to address nf-core#1496

Bit scared it'll break something, so ideally needs extensive testing.
@ewels ewels mentioned this issue Mar 29, 2022
Merged
4 tasks
ewels added a commit to ewels/nf-core-tools that referenced this issue Apr 6, 2022
@ewels
First stab at writing a central utils function for GitHub API calls.
2d99a43 
Uses authentication from local gh CLI or a supplied bearer token if found.

Done to address nf-core#1496

Bit scared it'll break something, so ideally needs extensive testing.
@maxulysse maxulysse added this to the 2.4 milestone May 5, 2022
@ewels ewels closed this as completed May 11, 2022
fabianegli pushed a commit to fabianegli/tools that referenced this issue May 12, 2022
@ewels @fabianegli
First stab at writing a central utils function for GitHub API calls.
90ec221 
Uses authentication from local gh CLI or a supplied bearer token if found.

Done to address nf-core#1496

Bit scared it'll break something, so ideally needs extensive testing.
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