chore(deps): update dependency snakemake to v9.13.2 #6304

renovate · 2025-10-07T18:02:18Z

This PR contains the following updates:

Package	Change	Age	Confidence
snakemake	`9.11.9` -> `9.13.2`

Release Notes

snakemake/snakemake (snakemake)

`v9.13.2`

Compare Source

Bug Fixes

fix --consider-ancient for input functions (was not applied in those cases) (#3788) (c28da7c)
only modify wrapper URI if imported rule actually uses a wrapper (#3790) (08ef3b4)

`v9.13.1`

Compare Source

Bug Fixes

config: restore $ref resolution for schemas (#3777) (a3e0939)
fix iofile formatting to always display the storage query if it is set, also in case of missing input exceptions (#3786) (b1c29fa)

`v9.13.0`

Compare Source

Features

expect meta-wrapper snakefile in meta_wrapper.smk (#3785) (843948d)

Bug Fixes

re-evaluate until and omit-from after checkpoint updates (#3773) (2eb9079)

`v9.12.0`

Compare Source

Features

introduce pathvars, allowing to configure parts of input/output/log/benchmark paths for the entire workflow, per module, or per rule (#3760) (e376a25)

Configuration

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

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github-actions · 2025-10-07T18:11:37Z

✅⚠️MegaLinter analysis: Success with warnings

⚠️ PYTHON / bandit - 68 errors

Run started:2025-10-12 09:54:34.265578

Test results:
>> Issue: [B404:blacklist] Consider possible security implications associated with the subprocess module.
   Severity: Low   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/blacklists/blacklist_imports.html#b404-import-subprocess
   Location: ./.automation/build.py:11:0
10	import shutil
11	import subprocess
12	import sys

--------------------------------------------------
>> Issue: [B105:hardcoded_password_string] Possible hardcoded password: ''
   Severity: Low   Confidence: Medium
   CWE: CWE-259 (https://cwe.mitre.org/data/definitions/259.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b105_hardcoded_password_string.html
   Location: ./.automation/build.py:3064:35
3063	                api_github_headers = {"content-type": "application/json"}
3064	                use_github_token = ""
3065	                if "GITHUB_TOKEN" in os.environ:

--------------------------------------------------
>> Issue: [B105:hardcoded_password_string] Possible hardcoded password: ' (with GITHUB_TOKEN)'
   Severity: Low   Confidence: Medium
   CWE: CWE-259 (https://cwe.mitre.org/data/definitions/259.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b105_hardcoded_password_string.html
   Location: ./.automation/build.py:3068:39
3067	                    api_github_headers["authorization"] = f"Bearer {github_token}"
3068	                    use_github_token = " (with GITHUB_TOKEN)"
3069	                logging.info(

--------------------------------------------------
>> Issue: [B602:subprocess_popen_with_shell_equals_true] subprocess call with shell=True identified, security issue.
   Severity: High   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b602_subprocess_popen_with_shell_equals_true.html
   Location: ./.automation/build.py:3445:14
3444	        cwd=cwd,
3445	        shell=True,
3446	        executable=None if sys.platform == "win32" else which("bash"),
3447	    )
3448	    stdout = utils.clean_string(process.stdout)
3449	    logging.info(f"Format table results: ({process.returncode})\n" + stdout)
3450	
3451	
3452	def generate_version():
3453	    # npm version
3454	    logging.info("Updating npm package version…")

--------------------------------------------------
>> Issue: [B607:start_process_with_partial_path] Starting a process with a partial executable path
   Severity: Low   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b607_start_process_with_partial_path.html
   Location: ./.automation/build.py:3456:14
3455	    cwd_to_use = os.getcwd() + "/mega-linter-runner"
3456	    process = subprocess.run(
3457	        [
3458	            "npm",
3459	            "version",
3460	            "--newversion",
3461	            RELEASE_TAG,
3462	            "-no-git-tag-version",
3463	            "--no-commit-hooks",
3464	        ],
3465	        stdout=subprocess.PIPE,
3466	        universal_newlines=True,
3467	        cwd=cwd_to_use,
3468	        shell=True,
3469	    )
3470	    print(process.stdout)

--------------------------------------------------
>> Issue: [B602:subprocess_popen_with_shell_equals_true] subprocess call with shell=True identified, security issue.
   Severity: High   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b602_subprocess_popen_with_shell_equals_true.html
   Location: ./.automation/build.py:3468:14
3467	        cwd=cwd_to_use,
3468	        shell=True,
3469	    )
3470	    print(process.stdout)
3471	    print(process.stderr)
3472	    # Update python project version:
3473	    process = subprocess.run(
3474	        ["hatch", "version", RELEASE_TAG],
3475	        stdout=subprocess.PIPE,
3476	        text=True,
3477	        shell=True,
3478	        check=True,
3479	    )
3480	    # Update changelog
3481	    if UPDATE_CHANGELOG is True:
3482	        changelog_file = f"{REPO_HOME}/CHANGELOG.md"

--------------------------------------------------
>> Issue: [B607:start_process_with_partial_path] Starting a process with a partial executable path
   Severity: Low   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b607_start_process_with_partial_path.html
   Location: ./.automation/build.py:3473:14
3472	    # Update python project version:
3473	    process = subprocess.run(
3474	        ["hatch", "version", RELEASE_TAG],
3475	        stdout=subprocess.PIPE,
3476	        text=True,
3477	        shell=True,
3478	        check=True,
3479	    )
3480	    # Update changelog

--------------------------------------------------
>> Issue: [B602:subprocess_popen_with_shell_equals_true] subprocess call with shell=True identified, security issue.
   Severity: High   Confidence: High
   CWE: CWE-78 (https://cwe.mitre.org/data/definitions/78.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/plugins/b602_subprocess_popen_with_shell_equals_true.html
   Location: ./.automation/build.py:3477:14
3476	        text=True,
3477	        shell=True,
3478	        check=True,
3479	    )
3480	    # Update changelog
3481	    if UPDATE_CHANGELOG is True:
3482	        changelog_file = f"{REPO_HOME}/CHANGELOG.md"
3483	        with open(changelog_file, "r", encoding="utf-8") as md_file:
3484	            changelog_content = md_file.read()

--------------------------------------------------
>> Issue: [B60

(Truncated to 5714 characters out of 43076)

⚠️ BASH / bash-exec - 1 error

Results of bash-exec linter (version 5.2.37)
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 - 31 errors

[0000]  WARN no explicit name and version provided for directory source, deriving artifact ID from the given path (which is not ideal)
NAME                           INSTALLED  FIXED IN  TYPE    VULNERABILITY        SEVERITY  EPSS           RISK   
ejs                            3.1.6      3.1.7     npm     GHSA-phwq-j96m-2c2q  Critical  93.4% (99th)   87.8   
tar                            6.0.1      6.1.1     npm     GHSA-3jfq-g458-7qm9  High      85.5% (99th)   67.1   
requests                       2.24.0     2.31.0    python  GHSA-j8r2-6x86-q33q  Medium    6.3% (90th)    3.5    
ip                             1.1.5                npm     GHSA-2p57-rm9w-gvfp  High      2.8% (85th)    2.2    
minimist                       1.2.5      1.2.6     npm     GHSA-xvch-5gv4-984h  Critical  0.9% (74th)    0.8    
ejs                            3.1.6      3.1.10    npm     GHSA-ghr5-ch3p-vcr6  Medium    1.3% (78th)    0.6    
tar                            6.0.1      6.1.9     npm     GHSA-5955-9wpr-37jh  High      0.6% (68th)    0.5    
node-fetch                     2.6.6      2.6.7     npm     GHSA-r683-j2x4-v87g  High      0.5% (65th)    0.4    
minimatch                      3.0.4      3.0.5     npm     GHSA-f8q6-p94x-37v3  High      0.5% (63rd)    0.3    
semver                         7.3.5      7.5.2     npm     GHSA-c2qf-rxjj-qqgw  High      0.3% (54th)    0.2    
braces                         3.0.2      3.0.3     npm     GHSA-grv7-fg5c-xmjg  High      0.2% (45th)    0.2    
ansi-regex                     3.0.0      3.0.1     npm     GHSA-93q8-gq69-wqmw  High      0.2% (44th)    0.2    
@octokit/request-error         2.1.0      5.1.1     npm     GHSA-xx4v-prfh-6cgc  Medium    0.3% (53rd)    0.2    
@octokit/request               5.6.2      8.4.1     npm     GHSA-rmvr-2pp2-xj38  Medium    0.3% (50th)    0.1    
tar                            6.0.1      6.1.2     npm     GHSA-r628-mhmh-qjhw  High      0.2% (39th)    0.1    
http-cache-semantics           4.1.0      4.1.1     npm     GHSA-rc47-6667-2j5j  High      0.2% (37th)    0.1    
ip                             1.1.5      1.1.9     npm     GHSA-78xj-cgh5-2h22  Low       0.4% (59th)    0.1    
tar                            6.0.1      6.2.1     npm     GHSA-f5x3-32g6-xq36  Medium    0.2% (42nd)    0.1    
tar                            6.1.11     6.2.1     npm     GHSA-f5x3-32g6-xq36  Medium    0.2% (42nd)    0.1    
cross-spawn                    7.0.3      7.0.5     npm     GHSA-3xgq-45jj-v275  High      0.1% (33rd)    < 0.1  
@octokit/plugin-paginate-rest  2.17.0     9.2.2     npm     GHSA-h5c3-5r3r-rr8q  Medium    0.1% (33rd)    < 0.1  
micromatch                     4.0.4      4.0.8     npm     GHSA-952p-6rrq-rcjv  Medium    0.1% (32nd)    < 0.1  
requests                       2.24.0     2.32.4    python  GHSA-9hjg-9r4m-mvj7  Medium    0.1% (29th)    < 0.1  
debug                          4.2.0      4.3.1     npm     GHSA-gxpj-cx7g-858c  Low       < 0.1% (27th)  < 0.1  
requests                       2.24.0     2.32.0    python  GHSA-9wx4-h78v-vm56  Medium    < 0.1% (13th)  < 0.1  
tar                            6.0.1      6.1.7     npm     GHSA-9r2w-394v-53qc  High      < 0.1% (7th)   < 0.1  
word-wrap                      1.2.3      1.2.4     npm     GHSA-j8xg-fqg3-53r7  Medium    < 0.1% (12th)  < 0.1  
tar                            6.0.1      6.1.9     npm     GHSA-qq89-hq3f-393p  High      < 0.1% (4th)   < 0.1  
tmp                            0.0.33     0.2.4     npm     GHSA-52f5-9888-hmc6  Low       < 0.1% (18th)  < 0.1  
brace-expansion                1.1.11     1.1.12    npm     GHSA-v6h2-p8h4-qcjw  Low       < 0.1% (5th)   < 0.1  
brace-expansion                2.0.1      2.0.2     npm     GHSA-v6h2-p8h4-qcjw  Low       < 0.1% (5th)   < 0.1
[0032] ERROR discovered vulnerabilities at or above the severity threshold

⚠️ SPELL / lychee - 14 errors

[WARN ] WARNING: `--exclude-mail` is deprecated and will soon be removed; E-Mail is no longer checked by default. Use `--include-mail` to enable E-Mail checking.
[403] https://cloudtuned.hashnode.dev/ | Network error: Forbidden
[403] https://cloudtuned.hashnode.dev/introducing-megalinter-streamlining-code-quality-checks-across-multiple-languages | Network error: Forbidden
[403] https://npmjs.org/package/mega-linter-runner | Network error: Forbidden
[403] https://htmlhint.com/integrations/task-runner/ | Network error: Forbidden
[403] https://npmjs.org/package/mega-linter-runner | Error (cached)
[403] https://htmlhint.com/integrations/task-runner/ | Error (cached)
[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://www.npmjs.com/package/markdown-table-formatter | Network error: Forbidden
[404] https://plugins.jetbrains.com/plugin/11563-flake8-support | Network error: Not Found
[404] https://marketplace.visualstudio.com/items?itemName=ForceConfigControl.lightningflowscanner | Network error: Not Found
[404] https://raw.githubusercontent.com/Lightning-Flow-Scanner/.github/main/docs/images/bannerslim.png | Network error: Not Found
[404] https://raku.org/camelia-logo.png | Network error: Not Found
[TIMEOUT] https://www.gnu.org/software/bash/ | Timeout
[TIMEOUT] https://www.gnu.org/software/bash/manual/bash.html | Timeout
[TIMEOUT] https://www.nongnu.org/chktex | Timeout
[TIMEOUT] https://www.nongnu.org/chktex/ | Timeout
📝 Summary
---------------------
🔍 Total.........2374
✅ Successful....1893
⏳ Timeouts.........4
🔀 Redirected.......0
👻 Excluded.......463
❓ Unknown..........0
🚫 Errors..........14

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

Errors in megalinter/descriptors/latex.megalinter-descriptor.yml
[TIMEOUT] https://www.nongnu.org/chktex/ | Timeout
[TIMEOUT] https://www.nongnu.org/chktex | Timeout

Errors in megalinter/descriptors/salesforce.megalinter-descriptor.yml
[404] https://marketplace.visualstudio.com/items?itemName=ForceConfigControl.lightningflowscanner | Network error: Not Found
[404] https://raw.githubusercontent.com/Lightning-Flow-Scanner/.github/main/docs/images/bannerslim.png | Network error: Not Found

Errors in megalinter/descriptors/bash.megalinter-descriptor.yml
[TIMEOUT] https://www.gnu.org/software/bash/manual/bash.html | Timeout
[TIMEOUT] https://www.gnu.org/software/bash/ | Timeout

Errors in megalinter/descriptors/raku.megalinter-descriptor.yml
[404] https://raku.org/camelia-logo.png | Network error: Not Found

Errors in README.md
[403] https://cloudtuned.hashnode.dev/ | Network error: Forbidden
[403] https://npmjs.org/package/mega-linter-runner | Network error: 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

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

Errors in megalinter/descriptors/html.megalinter-descriptor.yml
[403] https://htmlhint.com/integrations/task-runner/ | Error (cached)
[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

Errors in megalinter/descriptors/python.megalinter-descriptor.yml
[404] https://plugins.jetbrains.com/plugin/11563-flake8-support | Network error: Not Found

⚠️ MARKDOWN / markdownlint - 312 errors

.github/copilot-instructions.md:9 MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/copilot-instructions.md:156 MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/linters/valestyles/proselint/README.md:12:601 MD013/line-length Line length [Expected: 600; Actual: 755]
CHANGELOG.md:47:90 MD059/descriptive-link-text Link text should be descriptive [Context: "[here]"]
CHANGELOG.md:2068:87 MD059/descriptive-link-text Link text should be descriptive [Context: "[here]"]
docs/articles.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "They talk about MegaLinter"]
docs/badge.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Badge"]
docs/config-activation.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Activation and deactivation"]
docs/config-apply-fixes.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Apply fixes"]
docs/config-cli-lint-mode.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "CLI lint mode"]
docs/config-file.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: ".mega-linter.yml file"]
docs/config-filtering.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Filter linted files"]
docs/config-linters.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Linter specific variables"]
docs/config-postcommands.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Post-commands"]
docs/config-precommands.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Pre-commands"]
docs/config-variables-security.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Environment variables security"]
docs/config-variables.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Common variables"]
docs/configuration.md:9 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "Configuration"]
docs/descriptors/action_actionlint.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "actionlint"]
docs/descriptors/action.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "ACTION"]
docs/descriptors/ansible_ansible_lint.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "ansible-lint"]
docs/descriptors/ansible_ansible_lint.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 795]
docs/descriptors/ansible.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "ANSIBLE"]
docs/descriptors/api_spectral.md:14:601 MD013/line-length Line length [Expected: 600; Actual: 746]
docs/descriptors/api.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "API"]
docs/descriptors/arm_arm_ttk.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "arm-ttk"]
docs/descriptors/arm.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "ARM"]
docs/descriptors/bash_bash_exec.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "bash-exec"]
docs/descriptors/bash_shellcheck.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "shellcheck"]
docs/descriptors/bash_shellcheck.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 785]
docs/descriptors/bash_shfmt.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "shfmt"]
docs/descriptors/bash.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "BASH"]
docs/descriptors/bicep_bicep_linter.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "bicep_linter"]
docs/descriptors/bicep.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "BICEP"]
docs/descriptors/c_clang_format.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "clang-format"]
docs/descriptors/c_clang_format.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 768]
docs/descriptors/c_cppcheck.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "cppcheck"]
docs/descriptors/c_cpplint.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "cpplint"]
docs/descriptors/c.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "C"]
docs/descriptors/clojure_cljstyle.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "cljstyle"]
docs/descriptors/clojure_cljstyle.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 768]
docs/descriptors/clojure.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "CLOJURE"]
docs/descriptors/cloudformation_cfn_lint.md:14:601 MD013/line-length Line length [Expected: 600; Actual: 865]
docs/descriptors/cloudformation.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "CLOUDFORMATION"]
docs/descriptors/coffee_coffeelint.md:7 MD025/single-title/single-h1 Multiple top-level headings 

(Truncated to 5714 characters out of 38821)

⚠️ YAML / prettier - 6 errors

.automation/plugins.yml 81ms (unchanged)
.github/FUNDING.yml 5ms (unchanged)
.github/dependabot.yml 38ms (unchanged)
.github/linters/.cfnlintrc.yml 2ms (unchanged)
.github/linters/.checkov.yml 4ms (unchanged)
.github/linters/.golangci.yml 8ms (unchanged)
.github/linters/.hadolint.yml 2ms (unchanged)
.github/linters/.openapirc.yml 2ms (unchanged)
.github/linters/.protolintrc.yml 9ms (unchanged)
.github/linters/.ruby-lint.yml 2ms (unchanged)
.github/linters/.yamllint.yml 7ms (unchanged)
.github/linters/analysis_options.yml 10ms (unchanged)
.github/linters/valestyles/Microsoft/AMPM.yml 5ms (unchanged)
.github/linters/valestyles/Microsoft/Accessibility.yml 4ms (unchanged)
.github/linters/valestyles/Microsoft/Acronyms.yml 12ms (unchanged)
.github/linters/valestyles/Microsoft/Adverbs.yml 28ms (unchanged)
.github/linters/valestyles/Microsoft/Auto.yml 7ms (unchanged)
.github/linters/valestyles/Microsoft/Avoid.yml 3ms (unchanged)
.github/linters/valestyles/Microsoft/ComplexWords.yml 29ms (unchanged)
.github/linters/valestyles/Microsoft/Contractions.yml 6ms (unchanged)
.github/linters/valestyles/Microsoft/Dashes.yml 11ms (unchanged)
.github/linters/valestyles/Microsoft/DateFormat.yml 2ms (unchanged)
.github/linters/valestyles/Microsoft/DateNumbers.yml 4ms (unchanged)
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cursor · 2025-10-12T09:52:03Z

flavors/java/Dockerfile

 ARG REPOSITORY_TRIVY_SBOM_VERSION=0.67.0
 # renovate: datasource=pypi depName=snakemake
-ARG PIP_SNAKEMAKE_VERSION=9.11.9
+ARG PIP_SNAKEMAKE_VERSION=9.13.2


Bug: Version Mismatch in PR Title and Code

The PR's title and description indicate updating snakemake to v9.13.1, but the code consistently updates it to v9.13.2. This version mismatch can cause confusion for reviewers and may lead to unexpected behavior or deployment issues.

Additional Locations (3)

flavors/python/Dockerfile#L182-L183

megalinter/descriptors/snakemake.megalinter-descriptor.yml#L41-L42

flavors/dotnet/Dockerfile#L178-L179

renovate bot added the dependencies Pull requests that update a dependency file label Oct 7, 2025

renovate bot requested review from Kurt-von-Laven, bdovaz, echoix and nvuillam as code owners October 7, 2025 18:02

renovate bot added the dependencies Pull requests that update a dependency file label Oct 7, 2025

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renovate bot force-pushed the renovate/snakemake-9.x branch from 8dda61c to 3049b1b Compare October 10, 2025 14:56

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renovate bot changed the title ~~chore(deps): update dependency snakemake to v9.12.0~~ chore(deps): update dependency snakemake to v9.13.0 Oct 10, 2025

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renovate bot force-pushed the renovate/snakemake-9.x branch from 3049b1b to 7c20496 Compare October 11, 2025 09:55

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renovate bot changed the title ~~chore(deps): update dependency snakemake to v9.13.0~~ chore(deps): update dependency snakemake to v9.13.1 Oct 11, 2025

chore(deps): update dependency snakemake to v9.13.2

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renovate bot force-pushed the renovate/snakemake-9.x branch from 7c20496 to f194fad Compare October 12, 2025 09:50

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renovate bot changed the title ~~chore(deps): update dependency snakemake to v9.13.1~~ chore(deps): update dependency snakemake to v9.13.2 Oct 12, 2025

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chore(deps): update dependency snakemake to v9.13.2 #6304

chore(deps): update dependency snakemake to v9.13.2 #6304

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chore(deps): update dependency snakemake to v9.13.2 #6304

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Release Notes

v9.13.2

Bug Fixes

v9.13.1

Bug Fixes

v9.13.0

Features

Bug Fixes

v9.12.0

Features

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Bug: Version Mismatch in PR Title and Code

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renovate bot commented Oct 7, 2025 •

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`v9.13.2`

`v9.13.1`

`v9.13.0`

`v9.12.0`

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