chore(deps): update dependency snakemake to v9.8.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Confidence
snakemake	9.7.1 -> 9.8.0

---

Release Notes

snakemake/snakemake (snakemake)

v9.8.0

Compare Source

Features

• add --no-temp flag synonymous to --notemp (#​3632) (c775634)

Bug Fixes

• fix exception when joining rule basedir to script or conda env path (#​3668) (347420c)

Documentation

• Update pixi setup section of tutorial (#​3664) (104203b)

---

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

---

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[github-actions]

🦙 MegaLinter status: ⚠️ WARNING

⚠️ PYTHON / bandit - 67 errors

Run started:2025-07-16 01:03:54.462939

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:2999:35
2998	                api_github_headers = {"content-type": "application/json"}
2999	                use_github_token = ""
3000	                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:3003:39
3002	                    api_github_headers["authorization"] = f"Bearer {github_token}"
3003	                    use_github_token = " (with GITHUB_TOKEN)"
3004	                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:3380:14
3379	        cwd=cwd,
3380	        shell=True,
3381	        executable=None if sys.platform == "win32" else which("bash"),
3382	    )
3383	    stdout = utils.clean_string(process.stdout)
3384	    logging.info(f"Format table results: ({process.returncode})\n" + stdout)
3385	
3386	
3387	def generate_version():
3388	    # npm version
3389	    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:3391:14
3390	    cwd_to_use = os.getcwd() + "/mega-linter-runner"
3391	    process = subprocess.run(
3392	        [
3393	            "npm",
3394	            "version",
3395	            "--newversion",
3396	            RELEASE_TAG,
3397	            "-no-git-tag-version",
3398	            "--no-commit-hooks",
3399	        ],
3400	        stdout=subprocess.PIPE,
3401	        universal_newlines=True,
3402	        cwd=cwd_to_use,
3403	        shell=True,
3404	    )
3405	    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:3403:14
3402	        cwd=cwd_to_use,
3403	        shell=True,
3404	    )
3405	    print(process.stdout)
3406	    print(process.stderr)
3407	    # Update python project version:
3408	    process = subprocess.run(
3409	        ["hatch", "version", RELEASE_TAG],
3410	        stdout=subprocess.PIPE,
3411	        text=True,
3412	        shell=True,
3413	        check=True,
3414	    )
3415	    # Update changelog
3416	    if UPDATE_CHANGELOG is True:
3417	        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:3408:14
3407	    # Update python project version:
3408	    process = subprocess.run(
3409	        ["hatch", "version", RELEASE_TAG],
3410	        stdout=subprocess.PIPE,
3411	        text=True,
3412	        shell=True,
3413	        check=True,
3414	    )
3415	    # 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:3412:14
3411	        text=True,
3412	        shell=True,
3413	        check=True,
3414	    )
3415	    # Update changelog
3416	    if UPDATE_CHANGELOG is True:
3417	        changelog_file = f"{REPO_HOME}/CHANGELOG.md"
3418	        with open(changelog_file, "r", encoding="utf-8") as md_file:
3419	            changelog_content = md_file.read()

--------------------------------------------------
>> Issue: [B605:start_process_with_a_shell] Starting a process with a shell, possible injection detected, 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/b605_start_process_with_a_shell.html
   Location: ./.automation/build.py:3460:4
3459	    logging.info("Running command: " + " ".join(command))
3460	    os.system(" ".join(command))
3461	

--------------------------------------------------
>> 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: ./megalinter/Linter.py:28:0
27	import shutil
28	import subprocess
29	import sys

--------------------------------------------------
>> Issue: [B310:blacklist] Audit url open for permitted schemes. Allowing use of file:/ or custom schemes is often unexpected.
   Severity: Medium   Confidence: High
   CWE: CWE-22 (https://cwe.mitre.org/data/definitions/22.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/blacklists/blacklist_calls.html#b310-urllib-urlopen
   Location: ./megalinter/Linter.py:567:24
566	                    with (
567	                        urllib.request.urlopen(remote_config_file) as response,
568	                        open(local_config_file, "wb") as out_file,

--------------------------------------------------
>> Issue: [B310:blacklist] Audit url open for permitted schemes. Allowing use of file:/ or custom schemes is often unexpected.
   Severity: Medium   Confidence: High
   CWE: CWE-22 (https://cwe.mitre.org/data/definitions/22.html)
   More Info: https://bandit.readthedocs.io/en/1.8.6/blacklists/blacklist_calls.html#b310-urllib-urlopen
   Location: ./megalinter/Linter.py:646:24
645	                    with (
646	                        urllib.request.urlopen(remote_ignore_file) as response,
647	                        open(local_ignore_file, "wb") as out_file,

--------------------------------------------------
>> Issue: [B602:subprocess_popen_with_shell_equals_true] subprocess call with shell=

(Truncated to 8000 characters out of 42362)

⚠️ 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 - 30 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  93.5% (99th)   87.9   
tar                            6.0.1      6.1.1     npm     GHSA-3jfq-g458-7qm9  High      86.8% (99th)   68.2   
requests                       2.24.0     2.31.0    python  GHSA-j8r2-6x86-q33q  Medium    6.1% (90th)    3.4    
ip                             1.1.5                npm     GHSA-2p57-rm9w-gvfp  High      2.6% (84th)    2.0    
minimist                       1.2.5      1.2.6     npm     GHSA-xvch-5gv4-984h  Critical  1.1% (77th)    1.1    
tar                            6.0.1      6.1.9     npm     GHSA-5955-9wpr-37jh  High      0.9% (75th)    0.7    
ejs                            3.1.6      3.1.10    npm     GHSA-ghr5-ch3p-vcr6  Medium    1.3% (78th)    0.6    
node-fetch                     2.6.6      2.6.7     npm     GHSA-r683-j2x4-v87g  High      0.6% (67th)    0.5    
minimatch                      3.0.4      3.0.5     npm     GHSA-f8q6-p94x-37v3  High      0.4% (61st)    0.3    
semver                         7.3.5      7.5.2     npm     GHSA-c2qf-rxjj-qqgw  High      0.4% (60th)    0.3    
tar                            6.0.1      6.1.2     npm     GHSA-r628-mhmh-qjhw  High      0.2% (43rd)    0.2    
ansi-regex                     3.0.0      3.0.1     npm     GHSA-93q8-gq69-wqmw  High      0.2% (42nd)    0.1    
cross-spawn                    7.0.3      7.0.5     npm     GHSA-3xgq-45jj-v275  High      0.2% (42nd)    0.1    
http-cache-semantics           4.1.0      4.1.1     npm     GHSA-rc47-6667-2j5j  High      0.2% (39th)    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    
braces                         3.0.2      3.0.3     npm     GHSA-grv7-fg5c-xmjg  High      0.2% (37th)    0.1    
@octokit/request-error         2.1.0      5.1.1     npm     GHSA-xx4v-prfh-6cgc  Medium    0.2% (42nd)    0.1    
micromatch                     4.0.4      4.0.8     npm     GHSA-952p-6rrq-rcjv  Medium    0.2% (41st)    < 0.1  
@octokit/request               5.6.2      8.4.1     npm     GHSA-rmvr-2pp2-xj38  Medium    0.2% (40th)    < 0.1  
@octokit/plugin-paginate-rest  2.17.0     9.2.2     npm     GHSA-h5c3-5r3r-rr8q  Medium    < 0.1% (26th)  < 0.1  
requests                       2.24.0     2.32.4    python  GHSA-9hjg-9r4m-mvj7  Medium    < 0.1% (21st)  < 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  
brace-expansion                1.1.11     1.1.12    npm     GHSA-v6h2-p8h4-qcjw  Low       < 0.1% (18th)  < 0.1  
brace-expansion                2.0.1      2.0.2     npm     GHSA-v6h2-p8h4-qcjw  Low       < 0.1% (18th)  < 0.1  
tar                            6.0.1      6.1.9     npm     GHSA-qq89-hq3f-393p  High      < 0.1% (3rd)   < 0.1  
tar                            6.0.1      6.1.7     npm     GHSA-9r2w-394v-53qc  High      < 0.1% (3rd)   < 0.1  
word-wrap                      1.2.3      1.2.4     npm     GHSA-j8xg-fqg3-53r7  Medium    < 0.1% (5th)   < 0.1
[0037] ERROR discovered vulnerabilities at or above the severity threshold

⚠️ SPELL / lychee - 5 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://htmlhint.com/integrations/task-runner/ | Network error: Forbidden
[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/ | Network error: Forbidden
[403] https://htmlhint.com/configuration/ | Network error: Forbidden
[TIMEOUT] https://www.programmez.com/page-devcon/devcon-20-100-securite-qualite-du-code | Timeout
📝 Summary
---------------------
🔍 Total.........2349
✅ Successful....1891
⏳ Timeouts.........1
🔀 Redirected.......0
👻 Excluded.......452
❓ Unknown..........0
🚫 Errors...........5

Errors in README.md
[TIMEOUT] https://www.programmez.com/page-devcon/devcon-20-100-securite-qualite-du-code | Timeout
[403] https://htmlhint.com/integrations/task-runner/ | Network error: Forbidden

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

⚠️ MARKDOWN / markdownlint - 307 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:1988:87 MD059/descriptive-link-text Link text should be descriptive [Context: "[here]"]
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 in the same document [Context: "coffeelint"]
docs/descriptors/coffee_coffeelint.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 746]
docs/descriptors/coffee.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "COFFEE"]
docs/descriptors/copypaste.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "COPYPASTE"]
docs/descriptors/cpp_clang_format.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "clang-format"]
docs/descriptors/cpp_clang_format.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 768]
docs/descriptors/cpp_cppcheck.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "cppcheck"]
docs/descriptors/cpp_cpplint.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "cpplint"]
docs/descriptors/cpp.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "C++"]
docs/descriptors/csharp_csharpier.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "csharpier"]
docs/descriptors/csharp_csharpier.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 750]
docs/descriptors/csharp_dotnet_format.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "dotnet-format"]
docs/descriptors/csharp_roslynator.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "roslynator"]
docs/descriptors/csharp_roslynator.md:8:601 MD013/line-length Line length [Expected: 600; Actual: 770]
docs/descriptors/csharp.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "C\#"]
docs/descriptors/css_stylelint.md:14:601 MD013/line-length Line length [Expected: 600; Actual: 788]
docs/descriptors/css.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "CSS"]
docs/descriptors/dart_dartanalyzer.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "dartanalyzer"]
docs/descriptors/dart.md:8 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "DART"]
docs/descriptors/dockerfile_hadolint.md:7 MD025/single-title/single-h1 Multiple top-level headings in the same document [Context: "hadolint"]
docs/descriptors/dockerfile_hadolint.md:8:601 MD013/line-length Line length [Expected: 600;

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✅ Linters with no issues

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

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