feat: update github actions workflow #9
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feat: complete minimal workflow as template
WalkthroughThis pull request introduces a comprehensive update to a Snakemake-based genomic data processing workflow. The changes span multiple configuration files, GitHub Actions workflows, and workflow scripts. Key modifications include updating workflow configurations, adding new environment definitions, introducing schema validations, and enhancing documentation. The workflow now supports genome data retrieval, read simulation, quality control, adapter trimming, and multi-sample report generation with improved modularity and configuration management. Changes
Sequence DiagramsequenceDiagram
participant User
participant Workflow
participant NCBI
participant Genome
participant Reads
participant QC
participant Trimming
participant Report
User->>Workflow: Configure parameters
Workflow->>NCBI: Retrieve genome data
NCBI-->>Genome: Download FASTA/GFF
Workflow->>Reads: Simulate sequencing reads
Reads->>QC: Perform quality check
QC->>Trimming: Trim adapters
Trimming->>Report: Generate MultiQC report
Report-->>User: Workflow complete
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Actionable comments posted: 6
♻️ Duplicate comments (1)
config/config.yml (1)
8-14:⚠️ Potential issueFix duplicate keys in gff_source_type configuration.
Same issue as in test config - duplicate "RefSeq" keys will cause data loss.
🧹 Nitpick comments (12)
workflow/Snakefile (1)
32-33: Enhance error handling in the onerror hook.The error message could be more informative by including the error details.
- print("--- An error occurred! ---") + print("--- An error occurred! ---") + print(f"Error: {workflow.logger.get_error_message()}") + print("Check the log files in the results directory for more details.")workflow/rules/process_reads.smk (1)
90-90: Consider adjusting thread allocation for cutadapt.Using 25% of total cores might be excessive for smaller files. Consider setting a maximum limit.
- threads: int(workflow.cores * 0.25) + threads: min(8, max(1, int(workflow.cores * 0.25)))workflow/scripts/get_genome.py (1)
61-61: Improve code style and readability.Several style improvements can be made:
- Use
not ininstead ofnot ... in- Simplify dict key checks
- if not "Name" in rec_keys: + if "Name" not in rec_keys: - if not "ID" in rec_keys: + if "ID" not in rec_keys: - for k in ncbi_genome.keys(): + for k in ncbi_genome:Also applies to: 72-72, 107-107
🧰 Tools
🪛 Ruff (0.8.2)
61-61: Test for membership should be
not inConvert to
not in(E713)
.test/config/multiqc_config.yml (1)
2-2: Add newline at end of file.Add a newline character at the end of the file to comply with YAML best practices.
🧰 Tools
🪛 yamllint (1.35.1)
[error] 2-2: no new line character at the end of file
(new-line-at-end-of-file)
config/schemas/samples.schema.yml (1)
1-25: Consider adding additional schema validations.The schema is well-structured, but could benefit from additional validations:
- Pattern validation for sample names (e.g., no spaces/special chars)
- Minimum value for replicate (e.g., >= 1)
- Pattern validation for read files (e.g., must end in .fastq.gz)
Example additions:
sample: type: string description: sample name/identifier + pattern: "^[A-Za-z0-9_-]+$" replicate: type: number default: 1 description: consecutive numbers representing multiple replicates of one condition + minimum: 1 read1: type: string description: names of fastq.gz files, read 1 + pattern: ".*\\.fastq\\.gz$" read2: type: string description: names of fastq.gz files, read 2 (optional) + pattern: ".*\\.fastq\\.gz$"config/schemas/config.schema.yml (3)
8-20: Add type and required field definitions for theget_genomeobject.The schema for
get_genomeshould specify its type and required fields for better validation.get_genome: + type: object properties: database: type: ["string", "null"] + enum: ["manual", "ncbi"] assembly: type: ["string", "null"] + pattern: "^GC[F|A]_[0-9]+\\.[0-9]+$" fasta: type: ["string", "null"] gff: type: ["string", "null"] gff_source_type: type: array + items: + type: string + required: ["database"]
21-28: Add constraints for numeric fields insimulate_reads.The schema for
simulate_readsshould include minimum/maximum constraints for numeric fields to prevent invalid values.simulate_reads: + type: object properties: read_length: type: number + minimum: 1 + maximum: 1000 read_number: type: number + minimum: 1 random_freq: type: number + minimum: 0 + maximum: 1 + required: ["read_length", "read_number", "random_freq"]
30-37: Add pattern validation for adapter sequences.The schema for
cutadaptshould include pattern validation for adapter sequences to ensure they contain valid nucleotide sequences.cutadapt: + type: object properties: threep_adapter: type: string + pattern: "^-a [ATCG]+$" fivep_adapter: type: string + pattern: "^-A [ATCG]+$" default: type: array + items: + type: string + required: ["threep_adapter", "fivep_adapter"].github/workflows/main.yml (1)
49-51: Consider adding test artifacts retention.Consider adding artifact retention for test results to help with debugging pipeline failures.
directory: .test snakefile: workflow/Snakefile args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache" + - uses: actions/upload-artifact@v4 + if: always() + with: + name: test-results + path: .test/results + retention-days: 14config/README.md (1)
73-73: Fix code span formatting.Remove extra spaces inside code spans to comply with Markdown formatting rules.
-[`-q 10 `, `-m 25 `, `-M 100`, `--overlap=5`] +[`-q 10`, `-m 25`, `-M 100`, `--overlap=5`]🧰 Tools
🪛 Markdownlint (0.37.0)
73-73: null
Spaces inside code span elements(MD038, no-space-in-code)
73-73: null
Spaces inside code span elements(MD038, no-space-in-code)
README.md (1)
117-122: Update list formatting for consistency.Convert asterisks to dashes for consistent unordered list formatting.
-* Replace `<owner>` and `<repo>` everywhere in the template -* Replace `<name>` with the workflow name -* Replace `<description>` with a description -* Update the workflow description -* Update the `README.md` badges +- Replace `<owner>` and `<repo>` everywhere in the template +- Replace `<name>` with the workflow name +- Replace `<description>` with a description +- Update the workflow description +- Update the `README.md` badges🧰 Tools
🪛 LanguageTool
[style] ~119-~119: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ...w name (can be the same as<repo>). * Replace<description>with a description of w...(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
🪛 Markdownlint (0.37.0)
117-117: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
118-118: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
119-119: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
120-120: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
121-121: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
122-122: Expected: dash; Actual: asterisk
Unordered list style(MD004, ul-style)
config/multiqc_config.yml (1)
1-2: Add newline at end of file.Add a newline character at the end of the file to comply with YAML formatting standards.
remove_sections: - samtools-stats +🧰 Tools
🪛 yamllint (1.35.1)
[error] 2-2: no new line character at the end of file
(new-line-at-end-of-file)
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⛔ Files ignored due to path filters (1)
.test/config/samples.tsvis excluded by!**/*.tsv
📒 Files selected for processing (21)
.github/workflows/conventional-prs.yml(2 hunks).github/workflows/main.yml(2 hunks).github/workflows/release-please.yml(1 hunks).gitignore(1 hunks).test/config/config.yml(1 hunks).test/config/multiqc_config.yml(1 hunks)README.md(1 hunks)config/README.md(1 hunks)config/config.yml(1 hunks)config/multiqc_config.yml(1 hunks)config/schemas/config.schema.yml(1 hunks)config/schemas/samples.schema.yml(1 hunks)workflow/Snakefile(1 hunks)workflow/envs/cutadapt.yml(1 hunks)workflow/envs/fastqc.yml(1 hunks)workflow/envs/get_genome.yml(1 hunks)workflow/envs/multiqc.yml(1 hunks)workflow/envs/simulate_reads.yml(1 hunks)workflow/rules/common.smk(1 hunks)workflow/rules/process_reads.smk(1 hunks)workflow/scripts/get_genome.py(1 hunks)
✅ Files skipped from review due to trivial changes (7)
- workflow/envs/multiqc.yml
- workflow/envs/get_genome.yml
- workflow/envs/fastqc.yml
- workflow/envs/simulate_reads.yml
- .gitignore
- .github/workflows/release-please.yml
- workflow/envs/cutadapt.yml
🧰 Additional context used
🪛 yamllint (1.35.1)
.test/config/multiqc_config.yml
[error] 2-2: no new line character at the end of file
(new-line-at-end-of-file)
config/multiqc_config.yml
[error] 2-2: no new line character at the end of file
(new-line-at-end-of-file)
🪛 LanguageTool
config/README.md
[style] ~81-~81: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ...w name (can be the same as <repo>). * Replace <description> with a description of w...
(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
README.md
[uncategorized] ~53-~53: You might be missing the article “the” here.
Context: ...### Execution To run the workflow from command line, change the working directory. ``...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
[style] ~119-~119: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ...w name (can be the same as <repo>). * Replace <description> with a description of w...
(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
🪛 Markdownlint (0.37.0)
config/README.md
73-73: null
Spaces inside code span elements
(MD038, no-space-in-code)
73-73: null
Spaces inside code span elements
(MD038, no-space-in-code)
README.md
117-117: Expected: dash; Actual: asterisk
Unordered list style
(MD004, ul-style)
118-118: Expected: dash; Actual: asterisk
Unordered list style
(MD004, ul-style)
119-119: Expected: dash; Actual: asterisk
Unordered list style
(MD004, ul-style)
120-120: Expected: dash; Actual: asterisk
Unordered list style
(MD004, ul-style)
121-121: Expected: dash; Actual: asterisk
Unordered list style
(MD004, ul-style)
113-113: null
Bare URL used
(MD034, no-bare-urls)
100-100: null
Spaces inside code span elements
(MD038, no-space-in-code)
100-100: null
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🪛 Ruff (0.8.2)
workflow/scripts/get_genome.py
17-17: Undefined name snakemake
(F821)
18-18: Undefined name snakemake
(F821)
19-19: Undefined name snakemake
(F821)
20-20: Undefined name snakemake
(F821)
21-21: Undefined name snakemake
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22-22: Undefined name snakemake
(F821)
23-23: Undefined name snakemake
(F821)
24-24: Undefined name snakemake
(F821)
29-29: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
29-29: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
41-41: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
41-41: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
47-47: f-string without any placeholders
Remove extraneous f prefix
(F541)
55-55: Undefined name snakemake
(F821)
61-61: Test for membership should be not in
Convert to not in
(E713)
72-72: Test for membership should be not in
Convert to not in
(E713)
107-107: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
🪛 actionlint (1.7.4)
.github/workflows/main.yml
29-29: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
🔇 Additional comments (6)
workflow/rules/common.smk (1)
16-17: 🛠️ Refactor suggestionVerify schema paths and add error handling.
The schema paths are using relative paths (
../../config/schemas/). This could be problematic if the working directory changes. Consider:
- Using
workflow.source_path()for reliable path resolution- Adding error handling for missing schema files
-validate(samples, schema="../../config/schemas/samples.schema.yml") -validate(config, schema="../../config/schemas/config.schema.yml") +validate(samples, schema=workflow.source_path("../config/schemas/samples.schema.yml")) +validate(config, schema=workflow.source_path("../config/schemas/config.schema.yml")).test/config/multiqc_config.yml (1)
1-2: LGTM! Configuration looks valid.The removal of samtools-stats section from the MultiQC report is properly configured.
🧰 Tools
🪛 yamllint (1.35.1)
[error] 2-2: no new line character at the end of file
(new-line-at-end-of-file)
.github/workflows/conventional-prs.yml (1)
Line range hint
1-20: LGTM! Workflow updates follow best practices.Good improvements:
- Explicit permissions following principle of least privilege
- Updated action version for security
- Clear job naming
config/config.yml (1)
1-27: Verify path consistency between test and production configs.The paths differ between test and production configs:
- Test config:
config/samples.tsv- Production config:
.test/config/samples.tsv- Test config:
config/multiqc_config.yml- Production config:
config/multiqc_config.ymlPlease verify the correct paths and ensure consistency.
.github/workflows/main.yml (1)
40-43: Add missing job dependencies.The Testing job should depend on both Linting and Formatting jobs to ensure proper execution order.
config/README.md (1)
3-82: Complete the workflow description placeholders.Several placeholders need to be replaced with actual content:
<detailed description>on line 3<name>in the title🧰 Tools
🪛 LanguageTool
[style] ~81-~81: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym.
Context: ...w name (can be the same as<repo>). * Replace<description>with a description of w...(ENGLISH_WORD_REPEAT_BEGINNING_RULE)
🪛 Markdownlint (0.37.0)
73-73: null
Spaces inside code span elements(MD038, no-space-in-code)
73-73: null
Spaces inside code span elements(MD038, no-space-in-code)
| "cutadapt {params.threep_adapter} {params.fivep_adapter} --cores {threads} " | ||
| "-o {output.fastq1} -p {output.fastq2} {input.fastq1} {input.fastq1} > {log.stdout} 2> {log.stderr}" |
There was a problem hiding this comment.
Fix incorrect input file reference in cutadapt command.
The second input file reference is incorrect, causing the same file to be processed twice.
- "-o {output.fastq1} -p {output.fastq2} {input.fastq1} {input.fastq1} > {log.stdout} 2> {log.stderr}"
+ "-o {output.fastq1} -p {output.fastq2} {input.fastq1} {input.fastq2} > {log.stdout} 2> {log.stderr}"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| "cutadapt {params.threep_adapter} {params.fivep_adapter} --cores {threads} " | |
| "-o {output.fastq1} -p {output.fastq2} {input.fastq1} {input.fastq1} > {log.stdout} 2> {log.stderr}" | |
| "cutadapt {params.threep_adapter} {params.fivep_adapter} --cores {threads} " | |
| "-o {output.fastq1} -p {output.fastq2} {input.fastq1} {input.fastq2} > {log.stdout} 2> {log.stderr}" |
| def check_fasta(input_fasta, log=[], error=[]): | ||
| with open(input_fasta, "r") as fasta_file: | ||
| fasta = fasta_file.read() | ||
| n_items = fasta.count(">") | ||
| if n_items: | ||
| log += [f"Supplied fasta file '{input_fasta}' was found"] | ||
| log += [f"Supplied fasta file contains {n_items} items"] | ||
| else: | ||
| error += ["The supplied fasta file contains no valid entries starting with '>'"] | ||
| return fasta, log, error | ||
|
|
There was a problem hiding this comment.
Fix mutable default arguments and improve code style.
The functions use mutable default arguments which can lead to unexpected behavior.
-def check_fasta(input_fasta, log=[], error=[]):
+def check_fasta(input_fasta, log=None, error=None):
+ log = [] if log is None else log
+ error = [] if error is None else error
-def check_gff(input_gff, log=[], error=[]):
+def check_gff(input_gff, log=None, error=None):
+ log = [] if log is None else log
+ error = [] if error is None else errorAlso applies to: 41-82
🧰 Tools
🪛 Ruff (0.8.2)
29-29: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
29-29: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
| input_database = snakemake.params["database"] | ||
| input_assembly = snakemake.params["assembly"] | ||
| input_fasta = snakemake.params["fasta"] | ||
| input_gff = snakemake.params["gff"] | ||
| output_path = snakemake.output["path"] | ||
| output_fasta = snakemake.output["fasta"] | ||
| output_gff = snakemake.output["gff"] | ||
| output_log = snakemake.log["path"] |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add snakemake import and type hints.
The script uses the snakemake variable without importing it. Also, consider adding type hints for better code maintainability.
+from snakemake.script import Snakemake
+
+# Type hint for the snakemake object
+snakemake: Snakemake📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| input_database = snakemake.params["database"] | |
| input_assembly = snakemake.params["assembly"] | |
| input_fasta = snakemake.params["fasta"] | |
| input_gff = snakemake.params["gff"] | |
| output_path = snakemake.output["path"] | |
| output_fasta = snakemake.output["fasta"] | |
| output_gff = snakemake.output["gff"] | |
| output_log = snakemake.log["path"] | |
| from snakemake.script import Snakemake | |
| # Type hint for the snakemake object | |
| snakemake: Snakemake | |
| input_database = snakemake.params["database"] | |
| input_assembly = snakemake.params["assembly"] | |
| input_fasta = snakemake.params["fasta"] | |
| input_gff = snakemake.params["gff"] | |
| output_path = snakemake.output["path"] | |
| output_fasta = snakemake.output["fasta"] | |
| output_gff = snakemake.output["gff"] | |
| output_log = snakemake.log["path"] |
🧰 Tools
🪛 Ruff (0.8.2)
17-17: Undefined name snakemake
(F821)
18-18: Undefined name snakemake
(F821)
19-19: Undefined name snakemake
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20-20: Undefined name snakemake
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21-21: Undefined name snakemake
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23-23: Undefined name snakemake
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24-24: Undefined name snakemake
(F821)
| if input_database.lower() == "ncbi": | ||
| ncbi_result = getoutput( | ||
| f"datasets summary genome accession {input_assembly} --as-json-lines | " | ||
| + "dataformat tsv genome --fields accession,annotinfo-release-date,organism-name" | ||
| ) | ||
| if ncbi_result.startswith("Error"): | ||
| error += [ncbi_result] | ||
| error += [ | ||
| "The supplied refseq/genbank ID was not valid. Example for correct input: 'GCF_000009045.1'" | ||
| ] | ||
| elif len(ncbi_result) == 0: | ||
| error += [ | ||
| "The result from fetching NCBI genome data has zero length. Please check your internet connection!" | ||
| ] | ||
| else: | ||
| ncbi_genome = [ | ||
| i.split("\t") | ||
| for i in ncbi_result.split("\n") | ||
| if not (i.startswith("New version") or i.startswith("Warning")) | ||
| ] | ||
| ncbi_genome = dict(zip(ncbi_genome[0], ncbi_genome[1])) | ||
| log += ["Found the following genome(s):"] | ||
| for k in ncbi_genome.keys(): | ||
| log += ["{0}: {1}".format(k, ncbi_genome.get(k))] | ||
| refseq_id = ncbi_genome.get("Assembly Accession") | ||
| if not refseq_id.startswith("GCF_"): | ||
| error += ["The RefSeq ID '{0}' has no valid format.".format(refseq_id)] | ||
| ncbi_command = ( | ||
| f"datasets download genome accession {refseq_id}" | ||
| + f" --filename {output_path}/database.zip --include genome,gff3; " | ||
| + f"cd {output_path}; unzip database.zip; rm database.zip" | ||
| ) | ||
| copy_command = ( | ||
| f"cp {output_path}/ncbi_dataset/data/{refseq_id}/*.fna {output_fasta}; " | ||
| + f"cp {output_path}/ncbi_dataset/data/{refseq_id}/genomic.gff {output_gff}" | ||
| ) | ||
| index_command = f"samtools faidx {output_fasta}" | ||
| str_out = getoutput(ncbi_command) | ||
| str_cp = getoutput(copy_command) | ||
| # import and check files | ||
| fasta, log, error = check_fasta(output_fasta, log, error) | ||
| index_out = getoutput(index_command) | ||
| gff, log, error = check_gff(output_gff, log, error) | ||
| # write cleaned gff file | ||
| with open(output_gff, "w") as gff_out: | ||
| GFF.write(gff, gff_out) | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add timeout handling for NCBI API calls.
The script should handle potential timeouts when fetching data from NCBI.
+import requests.exceptions
+from subprocess import getoutput, run, PIPE, TimeoutError
+def execute_with_timeout(command, timeout=300):
+ try:
+ result = run(command, shell=True, stdout=PIPE, stderr=PIPE, timeout=timeout, text=True)
+ return result.stdout
+ except TimeoutError:
+ return "Error: Command timed out after {} seconds".format(timeout)
- ncbi_result = getoutput(
+ ncbi_result = execute_with_timeout(
f"datasets summary genome accession {input_assembly} --as-json-lines | "
+ "dataformat tsv genome --fields accession,annotinfo-release-date,organism-name"
)Committable suggestion skipped: line range outside the PR's diff.
🧰 Tools
🪛 Ruff (0.8.2)
107-107: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
| gff_source_type: | ||
| [ | ||
| "RefSeq": "gene", | ||
| "RefSeq": "pseudogene", | ||
| "RefSeq": "CDS", | ||
| "Protein Homology": "CDS", | ||
| ] |
There was a problem hiding this comment.
Fix duplicate keys in gff_source_type configuration.
The current structure has duplicate "RefSeq" keys which will cause only the last entry to be used. This means the "gene" and "pseudogene" entries will be lost.
Restructure the configuration to preserve all entries:
gff_source_type:
[
- "RefSeq": "gene",
- "RefSeq": "pseudogene",
- "RefSeq": "CDS",
+ {"source": "RefSeq", "type": "gene"},
+ {"source": "RefSeq", "type": "pseudogene"},
+ {"source": "RefSeq", "type": "CDS"},
"Protein Homology": "CDS",
]📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| gff_source_type: | |
| [ | |
| "RefSeq": "gene", | |
| "RefSeq": "pseudogene", | |
| "RefSeq": "CDS", | |
| "Protein Homology": "CDS", | |
| ] | |
| gff_source_type: | |
| [ | |
| {"source": "RefSeq", "type": "gene"}, | |
| {"source": "RefSeq", "type": "pseudogene"}, | |
| {"source": "RefSeq", "type": "CDS"}, | |
| "Protein Homology": "CDS", | |
| ] |
| directory: . | ||
| snakefile: workflow/Snakefile | ||
| args: "--lint" | ||
| - uses: actions/checkout@v2 |
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Update the checkout action version.
The runner of "actions/checkout@v2" action is outdated. Update to v4 for consistency with other jobs.
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - uses: actions/checkout@v2 | |
| - uses: actions/checkout@v4 |
🧰 Tools
🪛 actionlint (1.7.4)
29-29: the runner of "actions/checkout@v2" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
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