chore(deps): update dependency snakemake to v9.17.2 by renovate[bot] · Pull Request #7402 · oxsecurity/megalinter

renovate · 2026-03-15T02:34:48Z

This PR contains the following updates:

Package	Change	Age	Confidence
snakemake	`9.16.3` → `9.17.2`

Release Notes

snakemake/snakemake (snakemake)

`v9.17.2`

Compare Source

Bug Fixes

docs: simplify development instructions (#4073) (89e041d)
ensure that the snakemake-wrappers repo is properly cached when --wrapper-prefix is not specified (#4111) (7c82cde)

Documentation

prepare redirects in docs (#4106) (67d5ec4)

`v9.17.1`

Compare Source

Bug Fixes

correctly register module pathvars of the module of each rule (#4105) (111a3ee)
persistence-backend cli enum parsing (#4099) (11a62e7)

Documentation

Add note on profile and module usage (#4103) (ff5e0b4)

`v9.17.0`

Compare Source

Features

Allow storing snakemake metadata in files or databases (#4012) (dd75f31)
Allow to specify comparison command per-unit test (#3956) (b88171c)
job table ordered topological when run is started (#4018) (75cf506)
lambda functions for priority in rules (#3253) (d2aa226)
Make on... directive of modules accessible (#4050) (e9f2e1c)

Bug Fixes

adjust conda tests to not fail on apple silicon; fix #4040 (#4049) (f5b0142)
allow "--containerize apptainer" to output apptainer format instead of dockerfile (#4030) (f5cac30)
apptainer command not recognized when singularity is absent (#4010) (b8162e2)
capture stderr when tests fail (#3995) (97d74ba)
docs: make Data-dependent conditional execution a complete example (#4043) (3a1d7f2)
don't build the DAG when running unlock. Fixes #4000 and #198 (#4007) (acf79fd)
Ensure pixi tasks may be run as advertised (#4046) (88253c2)
fix checkpoint handling corner cases (#3870 and #3559) (#4015) (63f4257)
issue 3642 (#4054) (76e6fc2)
issue 3815 (#4026) (b0eec96)
logging None in shellcmd context causes error (#4064) (d0652cd)
lookup function returns default value for empty DataFrame queries (#4056) (f71de97)
make cache: omit-software a rule specific property (#4085) (034a9e7)
reduce number of tests leaving temporary files behind (#4033) (a3a1c97)
regression in dynamic resource handling (#4038) (f2c554a)
somewhat shorter announce message (#4080) (57efc71)

Performance Improvements

switch reretry with tenacity; decouple container classes (with Python 3.7 compat for old scripts) from rest of the codebase (enabling moving to newer python versions) (#4032) (ffb19e7)

Documentation

Add AI-assisted contributions policy to contributing guidelines (#4051) (dd70526)
codebase: Update & simplify plugin architecture section (#4052) (176cf63)
Correct workflow.source_path() description in documentation (#4036) (45883c5)
fixed wrong code example for collect() function (#4037) (5c85ed8)
Minor docs improvements (#4089) (29ea226)
switch to sphinx_design for tabs (#3976) (9674614)
typo in the migration table breaking a pip install command (#4024) (66f9dda)

Configuration

📅 Schedule: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

If you want to rebase/retry this PR, check this box

This PR was generated by Mend Renovate. View the repository job log.

github-actions · 2026-03-15T02:58:33Z

✅⚠️MegaLinter analysis: Success with warnings

⚠️ PYTHON / bandit - 81 errors

124:4
123	    )
124	    assert os.path.isdir(config.get(request_id, "DEFAULT_WORKSPACE")), (
125	        "DEFAULT_WORKSPACE "
126	        + config.get(request_id, "DEFAULT_WORKSPACE")
127	        + " is not a valid folder"
128	    )
129	

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:172:4
171	    tmp_report_folder = tempfile.gettempdir() + os.path.sep + str(uuid.uuid4())
172	    assert os.path.isdir(workspace), f"Test folder {workspace} is not existing"
173	    linter_name = linter.linter_name

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:238:4
237	    tmp_report_folder = tempfile.gettempdir() + os.path.sep + str(uuid.uuid4())
238	    assert os.path.isdir(workspace), f"Test folder {workspace} is not existing"
239	    if os.path.isfile(workspace + os.path.sep + "no_test_failure"):

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:487:4
486	    )
487	    assert os.path.isdir(workspace), f"Test folder {workspace} is not existing"
488	    expected_file_name = ""

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:587:4
586	        workspace += os.path.sep + "bad"
587	    assert os.path.isdir(workspace), f"Test folder {workspace} is not existing"
588	    # Call linter

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:676:4
675	        workspace = workspace + os.path.sep + "fix"
676	    assert os.path.isdir(workspace), f"Test folder {workspace} is not existing"
677	

--------------------------------------------------
>> Issue: [B101:assert_used] Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
   Severity: Low   Confidence: High
   CWE: CWE-703 (https://cwe.mitre.org/data/definitions/703.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b101_assert_used.html
   Location: ./megalinter/utilstest.py:782:12
781	            ]
782	            assert (len(list(diffs))) > 0, f"No changes in the {file} file"
783	

--------------------------------------------------
>> Issue: [B108:hardcoded_tmp_directory] Probable insecure usage of temp file/directory.
   Severity: Medium   Confidence: Medium
   CWE: CWE-377 (https://cwe.mitre.org/data/definitions/377.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b108_hardcoded_tmp_directory.html
   Location: ./server/server.py:81:42
80	    if item.fileUploadId:
81	        uploaded_file_path = os.path.join("/tmp/server-files", item.fileUploadId)
82	        if not os.path.isdir(uploaded_file_path):

--------------------------------------------------
>> Issue: [B108:hardcoded_tmp_directory] Probable insecure usage of temp file/directory.
   Severity: Medium   Confidence: Medium
   CWE: CWE-377 (https://cwe.mitre.org/data/definitions/377.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b108_hardcoded_tmp_directory.html
   Location: ./server/server.py:103:38
102	    file_upload_id = "FILE_" + str(uuid1())
103	    uploaded_file_path = os.path.join("/tmp/server-files", file_upload_id)
104	    os.makedirs(uploaded_file_path)

--------------------------------------------------
>> Issue: [B108:hardcoded_tmp_directory] Probable insecure usage of temp file/directory.
   Severity: Medium   Confidence: Medium
   CWE: CWE-377 (https://cwe.mitre.org/data/definitions/377.html)
   More Info: https://bandit.readthedocs.io/en/1.9.4/plugins/b108_hardcoded_tmp_directory.html
   Location: ./server/server_worker.py:98:34
97	        temp_dir = self.create_temp_dir()
98	        upload_dir = os.path.join("/tmp/server-files", file_upload_id)
99	        if os.path.exists(upload_dir):

--------------------------------------------------

Code scanned:
	Total lines of code: 17877
	Total lines skipped (#nosec): 0
	Total potential issues skipped due to specifically being disabled (e.g., #nosec BXXX): 0

Run metrics:
	Total issues (by severity):
		Undefined: 0
		Low: 48
		Medium: 24
		High: 9
	Total issues (by confidence):
		Undefined: 0
		Low: 16
		Medium: 18
		High: 47
Files skipped (0):

(Truncated to last 5714 characters out of 55563)

⚠️ BASH / bash-exec - 1 error

Results of bash-exec linter (version 5.3.3)
See documentation on https://megalinter.io/beta/descriptors/bash_bash_exec/
-----------------------------------------------

✅ [SUCCESS] .automation/build_schemas_doc.sh
✅ [SUCCESS] .automation/format-tables.sh
✅ [SUCCESS] .vscode/testlinter.sh
✅ [SUCCESS] build.sh
✅ [SUCCESS] entrypoint.sh
❌ [ERROR] sh/megalinter_exec
    Error: File:[sh/megalinter_exec] is not executable

⚠️ REPOSITORY / grype - 67 errors

GHSA-h5c3-5r3r-rr8q  Medium    0.2% (45th)    0.1    
@octokit/request-error         2.1.0      5.1.1     npm     GHSA-xx4v-prfh-6cgc  Medium    0.2% (43rd)    0.1    
simple-git                     3.27.0     3.32.3    npm     GHSA-r275-fr43-pm7q  Critical  < 0.1% (26th)  < 0.1  
tar                            6.0.1      6.1.7     npm     GHSA-9r2w-394v-53qc  High      0.1% (29th)    < 0.1  
@octokit/request               5.6.2      8.4.1     npm     GHSA-rmvr-2pp2-xj38  Medium    0.2% (36th)    < 0.1  
requests                       2.24.0     2.32.4    python  GHSA-9hjg-9r4m-mvj7  Medium    0.2% (35th)    < 0.1  
tar                            6.0.1      6.1.9     npm     GHSA-qq89-hq3f-393p  High      < 0.1% (24th)  < 0.1  
micromatch                     4.0.4      4.0.8     npm     GHSA-952p-6rrq-rcjv  Medium    0.1% (31st)    < 0.1  
cross-spawn                    7.0.3      7.0.5     npm     GHSA-3xgq-45jj-v275  High      < 0.1% (20th)  < 0.1  
minimatch                      3.0.4      3.1.3     npm     GHSA-3ppc-4f35-3m26  High      < 0.1% (16th)  < 0.1  
minimatch                      3.1.2      3.1.3     npm     GHSA-3ppc-4f35-3m26  High      < 0.1% (16th)  < 0.1  
minimatch                      5.1.6      5.1.7     npm     GHSA-3ppc-4f35-3m26  High      < 0.1% (16th)  < 0.1  
minimatch                      7.4.6      7.4.7     npm     GHSA-3ppc-4f35-3m26  High      < 0.1% (16th)  < 0.1  
minimatch                      9.0.5      9.0.6     npm     GHSA-3ppc-4f35-3m26  High      < 0.1% (16th)  < 0.1  
minimatch                      10.2.1     10.2.3    npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      3.0.4      3.1.3     npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      3.1.2      3.1.3     npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      5.1.6      5.1.8     npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      7.4.6      7.4.8     npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      9.0.5      9.0.7     npm     GHSA-7r86-cg39-jmmj  High      < 0.1% (16th)  < 0.1  
minimatch                      10.2.1     10.2.3    npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
minimatch                      3.0.4      3.1.4     npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
minimatch                      3.1.2      3.1.4     npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
minimatch                      5.1.6      5.1.8     npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
minimatch                      7.4.6      7.4.8     npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
minimatch                      9.0.5      9.0.7     npm     GHSA-23c5-xmqv-rm74  High      < 0.1% (16th)  < 0.1  
debug                          4.2.0      4.3.1     npm     GHSA-gxpj-cx7g-858c  Low       < 0.1% (26th)  < 0.1  
tmp                            0.0.33     0.2.4     npm     GHSA-52f5-9888-hmc6  Low       < 0.1% (24th)  < 0.1  
requests                       2.24.0     2.32.0    python  GHSA-9wx4-h78v-vm56  Medium    < 0.1% (13th)  < 0.1  
lodash                         4.17.21    4.17.23   npm     GHSA-xxjr-mmjv-4gpg  Medium    < 0.1% (6th)   < 0.1  
lodash-es                      4.17.21    4.17.23   npm     GHSA-xxjr-mmjv-4gpg  Medium    < 0.1% (6th)   < 0.1  
word-wrap                      1.2.3      1.2.4     npm     GHSA-j8xg-fqg3-53r7  Medium    < 0.1% (7th)   < 0.1  
tar                            6.0.1      7.5.7     npm     GHSA-34x7-hfp2-rc4v  High      < 0.1% (4th)   < 0.1  
tar                            6.1.11     7.5.7     npm     GHSA-34x7-hfp2-rc4v  High      < 0.1% (4th)   < 0.1  
tar                            6.0.1      7.5.10    npm     GHSA-qffp-2rhf-9h96  High      < 0.1% (3rd)   < 0.1  
tar                            6.1.11     7.5.10    npm     GHSA-qffp-2rhf-9h96  High      < 0.1% (3rd)   < 0.1  
js-yaml                        3.14.0     3.14.2    npm     GHSA-mh29-5h37-fv8m  Medium    < 0.1% (5th)   < 0.1  
tar                            6.0.1      7.5.8     npm     GHSA-83g3-92jg-28cx  High      < 0.1% (1st)   < 0.1  
tar                            6.1.11     7.5.8     npm     GHSA-83g3-92jg-28cx  High      < 0.1% (1st)   < 0.1  
brace-expansion                1.1.11     1.1.12    npm     GHSA-v6h2-p8h4-qcjw  Low       < 0.1% (8th)   < 0.1  
tar                            6.0.1      7.5.4     npm     GHSA-r6q2-hw4h-h46w  High      < 0.1% (0th)   < 0.1  
tar                            6.1.11     7.5.4     npm     GHSA-r6q2-hw4h-h46w  High      < 0.1% (0th)   < 0.1  
tar                            6.0.1      7.5.11    npm     GHSA-9ppj-qmqm-q256  High      < 0.1% (0th)   < 0.1  
tar                            6.1.11     7.5.11    npm     GHSA-9ppj-qmqm-q256  High      < 0.1% (0th)   < 0.1  
tar                            6.0.1      7.5.3     npm     GHSA-8qq5-rm4j-mr97  High      < 0.1% (0th)   < 0.1  
tar                            6.1.11     7.5.3     npm     GHSA-8qq5-rm4j-mr97  High      < 0.1% (0th)   < 0.1  
diff                           5.2.0      5.2.2     npm     GHSA-73rr-hh4g-fpgx  Low       < 0.1% (4th)   < 0.1  
diff                           7.0.0      8.0.3     npm     GHSA-73rr-hh4g-fpgx  Low       < 0.1% (4th)   < 0.1  
@tootallnate/once              1.1.2      3.0.1     npm     GHSA-vpq2-c234-7xj6  Low       < 0.1% (2nd)   < 0.1  
serialize-javascript           6.0.2      7.0.3     npm     GHSA-5c6j-r48x-rmvq  High      N/A            N/A
[0071] ERROR discovered vulnerabilities at or above the severity threshold

(Truncated to last 5714 characters out of 7967)

⚠️ SPELL / lychee - 26 errors

: Forbidden
[403] https://htmlhint.com/integrations/task-runner/ | Network error: Forbidden
[403] https://cloudtuned.hashnode.dev/introducing-megalinter-streamlining-code-quality-checks-across-multiple-languages | Network error: Forbidden
[403] https://pmd.sourceforge.io/pmd-6.55.0/pmd_userdocs_tools_ci.html | Network error: Forbidden
[403] https://cloudtuned.hashnode.dev/ | Network error: Forbidden
[404] https://github.com/$ | Network error: Not Found
[403] https://npmjs.org/package/mega-linter-runner | Error (cached)
[403] https://stackoverflow.com/a/73711302 | Network error: Forbidden
[403] https://stackoverflow.com/a/73711302 | Error (cached)
[403] https://cppcheck.sourceforge.io/manual.html#configuration | Network error: Forbidden
[403] https://cppcheck.sourceforge.io/ | Network error: Forbidden
[403] https://stackoverflow.com/a/73711302 | Network error: Forbidden
[403] https://cppcheck.sourceforge.io/manual.html#configuration | Network error: Forbidden
[403] https://cppcheck.sourceforge.io/ | Network error: Forbidden
[403] https://pmd.sourceforge.io/pmd-6.55.0/pmd_userdocs_tools_ci.html | Error (cached)
[ERROR] https://eslint.org/docs/latest/use/configure/rules#disabling-rules | Network error: error sending request for url (https://eslint.org/docs/latest/use/configure/rules#disabling-rules) Maybe a certificate error?
[ERROR] https://eslint.org/docs/latest/use/configure/rules#disabling-rules | Error (cached)
[403] https://htmlhint.com/integrations/task-runner/ | Error (cached)
[403] https://htmlhint.com/ | Network error: Forbidden
[403] https://htmlhint.com/configuration/ | Network error: Forbidden
[404] https://htmlhint.com/_astro/htmlhint.DIRCoA_t_Z1czEXa.webp | Network error: Not Found
[403] https://htmlhint.com/docs/user-guide/list-rules | Network error: Forbidden
[403] https://stackoverflow.com/a/73711302 | Error (cached)
[403] https://www.npmjs.com/package/markdown-table-formatter | Network error: Forbidden
[403] https://docutils.sourceforge.io/docs/ref/rst/directives.html#raw-data-pass-through | Network error: Forbidden
[406] https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home | Network error: Not Acceptable
[TIMEOUT] https://generated.at/ | Timeout
[TIMEOUT] https://generated.at/ | Timeout
📝 Summary
---------------------
🔍 Total.........2431
✅ Successful....1931
⏳ Timeouts.........2
🔀 Redirected.......0
👻 Excluded.......472
❓ Unknown..........0
🚫 Errors..........26

Errors in README.md
[403] https://cloudtuned.hashnode.dev/introducing-megalinter-streamlining-code-quality-checks-across-multiple-languages | Network error: Forbidden
[403] https://cloudtuned.hashnode.dev/ | Network error: Forbidden
[TIMEOUT] https://generated.at/ | Timeout
[403] https://htmlhint.com/integrations/task-runner/ | Network error: Forbidden
[403] https://npmjs.org/package/mega-linter-runner | Network error: Forbidden
[403] https://pmd.sourceforge.io/pmd-6.55.0/pmd_userdocs_tools_ci.html | Network error: Forbidden

Errors in megalinter/descriptors/jsx.megalinter-descriptor.yml
[ERROR] https://eslint.org/docs/latest/use/configure/rules#disabling-rules | Error (cached)

Errors in megalinter/descriptors/markdown.megalinter-descriptor.yml
[403] https://www.npmjs.com/package/markdown-table-formatter | Network error: Forbidden

Errors in megalinter/descriptors/cpp.megalinter-descriptor.yml
[403] https://cppcheck.sourceforge.io/manual.html#configuration | Network error: Forbidden
[403] https://cppcheck.sourceforge.io/ | Network error: Forbidden

Errors in megalinter/descriptors/rst.megalinter-descriptor.yml
[403] https://docutils.sourceforge.io/docs/ref/rst/directives.html#raw-data-pass-through | Network error: Forbidden

Errors in megalinter/descriptors/html.megalinter-descriptor.yml
[403] https://htmlhint.com/docs/user-guide/list-rules | Network error: Forbidden
[403] https://htmlhint.com/configuration/ | Network error: Forbidden
[403] https://htmlhint.com/ | Network error: Forbidden
[403] https://htmlhint.com/integrations/task-runner/ | Error (cached)
[404] https://htmlhint.com/_astro/htmlhint.DIRCoA_t_Z1czEXa.webp | Network error: Not Found

Errors in megalinter/descriptors/bicep.megalinter-descriptor.yml
[403] https://stackoverflow.com/a/73711302 | Network error: Forbidden

Errors in megalinter/descriptors/arm.megalinter-descriptor.yml
[403] https://stackoverflow.com/a/73711302 | Network error: Forbidden

Errors in megalinter/descriptors/javascript.megalinter-descriptor.yml
[ERROR] https://eslint.org/docs/latest/use/configure/rules#disabling-rules | Network error: error sending request for url (https://eslint.org/docs/latest/use/configure/rules#disabling-rules) Maybe a certificate error?

Errors in megalinter/descriptors/xml.megalinter-descriptor.yml
[406] https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home | Network error: Not Acceptable

Errors in mega-linter-runner/generators/mega-linter-custom-flavor/templates/check-new-megalinter-version.yml
[404] https://github.com/$ | Network error: Not Found

Errors in mega-linter-runner/README.md
[403] https://npmjs.org/package/mega-linter-runner | Error (cached)

Errors in megalinter/descriptors/clojure.megalinter-descriptor.yml
[403] https://stackoverflow.com/a/73711302 | Error (cached)

Errors in megalinter/descriptors/powershell.megalinter-descriptor.yml
[403] https://stackoverflow.com/a/73711302 | Error (cached)

Errors in megalinter/descriptors/java.megalinter-descriptor.yml
[403] https://pmd.sourceforge.io/pmd-6.55.0/pmd_userdocs_tools_ci.html | Error (cached)

Errors in megalinter/descriptors/c.megalinter-descriptor.yml
[403] https://cppcheck.sourceforge.io/manual.html#configuration | Network error: Forbidden
[403] https://cppcheck.sourceforge.io/ | Network error: Forbidden

(Truncated to last 5714 characters out of 5942)

⚠️ MARKDOWN / markdownlint - 334 errors

ngle-h1 Multiple top-level headings in the same document [Context: "IDE Configuration Reporter"]
docs/reporters/ConsoleReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Console Reporter"]
docs/reporters/EmailReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "E-mail Reporter"]
docs/reporters/FileIoReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "File.io Reporter"]
docs/reporters/GitHubCommentReporter.md:6 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "GitHub Comment Reporter"]
docs/reporters/GitHubCommentReporter.md:27:196 error MD056/table-column-count Table column count [Expected: 4; Actual: 3; Too few cells, row will be missing data]
docs/reporters/GitHubCommentReporter.md:27:46 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:27:174 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:27:196 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:28:179 error MD056/table-column-count Table column count [Expected: 4; Actual: 3; Too few cells, row will be missing data]
docs/reporters/GitHubCommentReporter.md:28:46 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:28:160 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:28:179 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:29:159 error MD056/table-column-count Table column count [Expected: 4; Actual: 3; Too few cells, row will be missing data]
docs/reporters/GitHubCommentReporter.md:29:48 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:29:143 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:29:159 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:30:171 error MD056/table-column-count Table column count [Expected: 4; Actual: 3; Too few cells, row will be missing data]
docs/reporters/GitHubCommentReporter.md:30:46 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:30:152 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubCommentReporter.md:30:171 error MD060/table-column-style Table column style [Table pipe does not align with header for style "aligned"]
docs/reporters/GitHubStatusReporter.md:6 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "GitHub Status Reporter"]
docs/reporters/GitlabCommentReporter.md:6 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Gitlab Comment Reporter"]
docs/reporters/JsonReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "JSON Reporter"]
docs/reporters/MarkdownSummaryReporter.md:6 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Markdown Summary Reporter"]
docs/reporters/SarifReporter.md:6 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "SARIF Reporter (beta)"]
docs/reporters/TapReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "TAP Reporter"]
docs/reporters/TextReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Text Reporter"]
docs/reporters/UpdatedSourcesReporter.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Updated Sources Reporter"]
docs/special-thanks.md:9 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Special thanks"]
docs/special-thanks.md:23:3 error MD045/no-alt-text Images should have alternate text (alt text)
docs/sponsor.md:5 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Sponsoring"]
docs/supported-linters.md:9 error MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Supported Linters"]
mega-linter-runner/generators/mega-linter-custom-flavor/templates/README.md:63 error MD024/no-duplicate-heading Multiple headings with the same content [Context: "How to use the custom flavor"]
mega-linter-runner/README.md:27:274 error MD051/link-fragments Link fragments should be valid [Context: "[**apply formatting and auto-fixes**](#apply-fixes)"]
mega-linter-runner/README.md:27:217 error MD051/link-fragments Link fragments should be valid [Context: "[**reports in several formats**](#reports)"]
README.md:190:127 error MD051/link-fragments Link fragments should be valid [Context: "[many additional features](#mega-linter-vs-super-linter)"]
README.md:1769:3 error MD045/no-alt-text Images should have alternate text (alt text)

(Truncated to last 5714 characters out of 43819)

⚠️ YAML / prettier - 6 errors

ed)
codecov.yml 5ms (unchanged)
mega-linter-runner/.eslintrc.yml 3ms (unchanged)
mega-linter-runner/.mega-linter.yml 9ms (unchanged)
mega-linter-runner/generators/mega-linter-custom-flavor/templates/action.yml 6ms (unchanged)
mega-linter-runner/generators/mega-linter-custom-flavor/templates/check-new-megalinter-version.yml 24ms (unchanged)
mega-linter-runner/generators/mega-linter-custom-flavor/templates/megalinter-custom-flavor-builder.yml 18ms (unchanged)
[error] mega-linter-runner/generators/mega-linter-custom-flavor/templates/megalinter-custom-flavor.yml: SyntaxError: Implicit map keys need to be followed by map values (6:1)
[error]   4 | label: <%= CUSTOM_FLAVOR_LABEL %>
[error]   5 | linters:
[error] > 6 | <%= CUSTOM_FLAVOR_LINTERS %>
[error]     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[error]   7 |
mega-linter-runner/generators/mega-linter/templates/.drone.yml 2ms (unchanged)
mega-linter-runner/generators/mega-linter/templates/.gitlab-ci.yml 5ms (unchanged)
mega-linter-runner/generators/mega-linter/templates/azure-pipelines.yml 6ms (unchanged)
mega-linter-runner/generators/mega-linter/templates/bitbucket-pipelines.yml 3ms (unchanged)
mega-linter-runner/generators/mega-linter/templates/concourse-task.yml 6ms (unchanged)
mega-linter-runner/generators/mega-linter/templates/mega-linter.yml 26ms (unchanged)
megalinter/descriptors/action.megalinter-descriptor.yml 12ms (unchanged)
megalinter/descriptors/ansible.megalinter-descriptor.yml 10ms (unchanged)
megalinter/descriptors/api.megalinter-descriptor.yml 12ms (unchanged)
megalinter/descriptors/arm.megalinter-descriptor.yml 5ms (unchanged)
megalinter/descriptors/bash.megalinter-descriptor.yml 20ms (unchanged)
megalinter/descriptors/bicep.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/c.megalinter-descriptor.yml 16ms (unchanged)
megalinter/descriptors/clojure.megalinter-descriptor.yml 14ms (unchanged)
megalinter/descriptors/cloudformation.megalinter-descriptor.yml 9ms (unchanged)
megalinter/descriptors/coffee.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/copypaste.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/cpp.megalinter-descriptor.yml 18ms (unchanged)
megalinter/descriptors/csharp.megalinter-descriptor.yml 23ms (unchanged)
megalinter/descriptors/css.megalinter-descriptor.yml 8ms (unchanged)
megalinter/descriptors/dart.megalinter-descriptor.yml 7ms (unchanged)
megalinter/descriptors/dockerfile.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/editorconfig.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/env.megalinter-descriptor.yml 2ms (unchanged)
megalinter/descriptors/gherkin.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/go.megalinter-descriptor.yml 10ms (unchanged)
megalinter/descriptors/graphql.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/groovy.megalinter-descriptor.yml 9ms (unchanged)
megalinter/descriptors/html.megalinter-descriptor.yml 15ms (unchanged)
megalinter/descriptors/java.megalinter-descriptor.yml 6ms (unchanged)
megalinter/descriptors/javascript.megalinter-descriptor.yml 24ms (unchanged)
megalinter/descriptors/json.megalinter-descriptor.yml 27ms (unchanged)
megalinter/descriptors/jsx.megalinter-descriptor.yml 6ms (unchanged)
megalinter/descriptors/kotlin.megalinter-descriptor.yml 7ms (unchanged)
megalinter/descriptors/kubernetes.megalinter-descriptor.yml 9ms (unchanged)
megalinter/descriptors/latex.megalinter-descriptor.yml 2ms (unchanged)
megalinter/descriptors/lua.megalinter-descriptor.yml 8ms (unchanged)
megalinter/descriptors/makefile.megalinter-descriptor.yml 8ms (unchanged)
megalinter/descriptors/markdown.megalinter-descriptor.yml 25ms (unchanged)
megalinter/descriptors/perl.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/php.megalinter-descriptor.yml 23ms (unchanged)
megalinter/descriptors/powershell.megalinter-descriptor.yml 16ms (unchanged)
megalinter/descriptors/protobuf.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/puppet.megalinter-descriptor.yml 4ms (unchanged)
megalinter/descriptors/python.megalinter-descriptor.yml 57ms (unchanged)
megalinter/descriptors/r.megalinter-descriptor.yml 14ms (unchanged)
megalinter/descriptors/raku.megalinter-descriptor.yml 5ms (unchanged)
megalinter/descriptors/repository.megalinter-descriptor.yml 84ms (unchanged)
megalinter/descriptors/robotframework.megalinter-descriptor.yml 5ms (unchanged)
megalinter/descriptors/rst.megalinter-descriptor.yml 13ms (unchanged)
megalinter/descriptors/ruby.megalinter-descriptor.yml 17ms (unchanged)
megalinter/descriptors/rust.megalinter-descriptor.yml 7ms (unchanged)
megalinter/descriptors/salesforce.megalinter-descriptor.yml 72ms (unchanged)
megalinter/descriptors/scala.megalinter-descriptor.yml 6ms (unchanged)
megalinter/descriptors/snakemake.megalinter-descriptor.yml 11ms (unchanged)
megalinter/descriptors/spell.megalinter-descriptor.yml 25ms (unchanged)
megalinter/descriptors/sql.megalinter-descriptor.yml 17ms (unchanged)
megalinter/descriptors/swift.megalinter-descriptor.yml 7ms (unchanged)
megalinter/descriptors/tekton.megalinter-descriptor.yml 5ms (unchanged)
megalinter/descriptors/terraform.megalinter-descriptor.yml 29ms (unchanged)
megalinter/descriptors/tsx.megalinter-descriptor.yml 7ms (unchanged)
megalinter/descriptors/typescript.megalinter-descriptor.yml 24ms (unchanged)
megalinter/descriptors/vbdotnet.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/xml.megalinter-descriptor.yml 3ms (unchanged)
megalinter/descriptors/yaml.megalinter-descriptor.yml 24ms (unchanged)
server/docker-compose-dev.yml 8ms (unchanged)
server/docker-compose.yml 6ms (unchanged)
trivy-secret.yaml 1ms (unchanged)

(Truncated to last 5714 characters out of 11504)

⚠️ YAML / yamllint - 31 errors

mega-linter-runner/.eslintrc.yml
  11:9      warning  too few spaces inside empty braces  (braces)

mega-linter-runner/generators/mega-linter-custom-flavor/templates/megalinter-custom-flavor.yml
  7:1       error    syntax error: could not find expected ':' (syntax)

megalinter/descriptors/copypaste.megalinter-descriptor.yml
  18:301    warning  line too long (313 > 300 characters)  (line-length)

megalinter/descriptors/javascript.megalinter-descriptor.yml
  234:301   warning  line too long (307 > 300 characters)  (line-length)

megalinter/descriptors/markdown.megalinter-descriptor.yml
  74:301    warning  line too long (366 > 300 characters)  (line-length)

megalinter/descriptors/perl.megalinter-descriptor.yml
  26:301    warning  line too long (310 > 300 characters)  (line-length)

megalinter/descriptors/php.megalinter-descriptor.yml
  149:301   warning  line too long (389 > 300 characters)  (line-length)
  163:301   warning  line too long (302 > 300 characters)  (line-length)

megalinter/descriptors/repository.megalinter-descriptor.yml
  155:301   warning  line too long (408 > 300 characters)  (line-length)
  268:301   warning  line too long (306 > 300 characters)  (line-length)
  273:301   warning  line too long (321 > 300 characters)  (line-length)
  450:301   warning  line too long (338 > 300 characters)  (line-length)
  518:301   warning  line too long (306 > 300 characters)  (line-length)
  568:301   warning  line too long (316 > 300 characters)  (line-length)
  818:301   warning  line too long (1263 > 300 characters)  (line-length)
  883:301   warning  line too long (879 > 300 characters)  (line-length)
  897:301   warning  line too long (358 > 300 characters)  (line-length)
  953:301   warning  line too long (346 > 300 characters)  (line-length)
  960:301   warning  line too long (307 > 300 characters)  (line-length)

megalinter/descriptors/salesforce.megalinter-descriptor.yml
  51:301    warning  line too long (359 > 300 characters)  (line-length)
  295:301   warning  line too long (359 > 300 characters)  (line-length)

megalinter/descriptors/spell.megalinter-descriptor.yml
  149:301   warning  line too long (315 > 300 characters)  (line-length)

megalinter/descriptors/sql.megalinter-descriptor.yml
  64:301    warning  line too long (319 > 300 characters)  (line-length)

megalinter/descriptors/terraform.megalinter-descriptor.yml
  27:301    warning  line too long (330 > 300 characters)  (line-length)
  86:301    warning  line too long (391 > 300 characters)  (line-length)
  142:301   warning  line too long (346 > 300 characters)  (line-length)
  199:301   warning  line too long (328 > 300 characters)  (line-length)

megalinter/descriptors/typescript.megalinter-descriptor.yml
  225:301   warning  line too long (314 > 300 characters)  (line-length)

mkdocs.yml
  8:301     warning  line too long (552 > 300 characters)  (line-length)
  66:5      warning  wrong indentation: expected 6 but found 4  (indentation)
  78:5      warning  wrong indentation: expected 6 but found 4  (indentation)

✅ Linters with no issues

black, checkov, cspell, flake8, git_diff, hadolint, isort, jscpd, jsonlint, markdown-table-formatter, mypy, npm-groovy-lint, pylint, ruff, secretlint, shellcheck, shfmt, spectral, syft, trivy, trivy-sbom, trufflehog, v8r, v8r, xmllint

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renovate bot added the dependencies Pull requests that update a dependency file label Mar 15, 2026

renovate bot requested review from Kurt-von-Laven, bdovaz, echoix and nvuillam as code owners March 15, 2026 02:34

renovate bot temporarily deployed to dev March 15, 2026 02:34 Inactive

chore(deps): update dependency snakemake to v9.17.2

e7a39f7

renovate bot force-pushed the renovate/snakemake-9.x branch from 34eb6c8 to e7a39f7 Compare March 17, 2026 17:16

renovate bot temporarily deployed to dev March 17, 2026 17:16 Inactive

renovate bot changed the title ~~chore(deps): update dependency snakemake to v9.17.1~~ chore(deps): update dependency snakemake to v9.17.2 Mar 17, 2026

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chore(deps): update dependency snakemake to v9.17.2#7402

chore(deps): update dependency snakemake to v9.17.2#7402
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Release Notes

v9.17.2

Bug Fixes

Documentation

v9.17.1

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v9.17.0

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`v9.17.2`

`v9.17.1`

`v9.17.0`

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