Feature/workflow #18
Feature/workflow #18
Conversation
📝 WalkthroughWalkthroughThe changes update the CI/CD workflow and introduce a new bioinformatics pipeline. The GitHub Actions workflow now includes a job for building a Docker image and linting both the Dockerfile and Snakefile, with the test job updated to depend on the Docker build. A new Changes
Sequence Diagram(s)sequenceDiagram
participant Repo as Repository
participant Docker as Docker-Build Job
participant Lint as Lint Job
participant Test as Test Job
Repo->>Docker: Checkout code, lint Dockerfile with hadolint, build Docker image
Docker->>Lint: Notify completion for Docker build
Repo->>Lint: Checkout code, lint Snakefile, run dry-run with Docker image
Docker->>Test: Signal dependency met for test job
Repo->>Test: Checkout code (v4) and run tests using Docker image
sequenceDiagram
participant A as Rule All
participant B as Rule bwa_map
participant C as Rule samtools_sort
participant D as Rule samtools_index
participant E as Rule bcftools_call
participant F as Rule plot_quals
participant S as plot-quals.py
A->>B: Trigger mapping step (generate BAM files)
B->>C: Pass BAM files for sorting
C->>D: Provide sorted BAM for indexing
D->>E: Supply inputs for variant calling
E->>F: Deliver VCF file for plotting
F->>S: Invoke Python script to generate quality plot (SVG)
Possibly related PRs
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Actionable comments posted: 0
🧹 Nitpick comments (10)
workflow/scripts/plot-quals.py (3)
6-7: Add error handling for the variant file inputThe script assumes the variant file exists and has quality scores, but doesn't include error handling.
-quals = [record.qual for record in VariantFile(snakemake.input[0])] -plt.hist(quals) +try: + vcf = VariantFile(snakemake.input[0]) + quals = [record.qual for record in vcf] + if not quals: + print("Warning: No quality scores found in the VCF file") + plt.hist(quals) +except Exception as e: + print(f"Error processing variant file: {e}") + raise🧰 Tools
🪛 Ruff (0.8.2)
6-6: Undefined name
snakemake(F821)
9-9: Add figure formatting before savingThe plot could benefit from labels and title for better interpretation.
-plt.savefig(snakemake.output[0]) +plt.xlabel('Quality Score') +plt.ylabel('Frequency') +plt.title('Distribution of Variant Quality Scores') +plt.tight_layout() +plt.savefig(snakemake.output[0])🧰 Tools
🪛 Ruff (0.8.2)
9-9: Undefined name
snakemake(F821)
1-9: Add a main guard for better script reusabilityThe script directly uses the
snakemakevariable which will cause errors if run outside of Snakemake.import matplotlib matplotlib.use("Agg") import matplotlib.pyplot as plt from pysam import VariantFile -quals = [record.qual for record in VariantFile(snakemake.input[0])] -plt.hist(quals) - -plt.savefig(snakemake.output[0]) +def plot_qualities(input_file, output_file): + try: + vcf = VariantFile(input_file) + quals = [record.qual for record in vcf] + if not quals: + print("Warning: No quality scores found in the VCF file") + plt.hist(quals) + plt.xlabel('Quality Score') + plt.ylabel('Frequency') + plt.title('Distribution of Variant Quality Scores') + plt.tight_layout() + plt.savefig(output_file) + except Exception as e: + print(f"Error processing variant file: {e}") + raise + +if __name__ == "__main__": + # This allows the script to be run both as a standalone script and through Snakemake + if 'snakemake' in globals(): + plot_qualities(snakemake.input[0], snakemake.output[0]) + else: + import sys + if len(sys.argv) != 3: + print("Usage: python plot-quals.py input.vcf output.svg") + sys.exit(1) + plot_qualities(sys.argv[1], sys.argv[2])🧰 Tools
🪛 Ruff (0.8.2)
6-6: Undefined name
snakemake(F821)
9-9: Undefined name
snakemake(F821)
workflow/Snakefile (4)
9-17: Consider adding threads parameter to bwa_map ruleBWA mem can benefit from parallelization, especially for larger datasets.
rule bwa_map: input: "data/genome.fa", "data/samples/{sample}.fastq", output: "mapped_reads/{sample}.bam", + threads: 4 shell: - "bwa mem {input} | samtools view -Sb - > {output}" + "bwa mem -t {threads} {input} | samtools view -Sb - > {output}"
19-27: Consider adding threads parameter to samtools_sort ruleSamtools sort can benefit from parallelization for improved performance.
rule samtools_sort: input: "mapped_reads/{sample}.bam", output: "sorted_reads/{sample}.bam", + threads: 4 shell: "samtools sort -T sorted_reads/{wildcards.sample} " - "-O bam {input} > {output}" + "-O bam -@ {threads} {input} > {output}"
38-48: Add parallel processing to bcftools commandsBoth mpileup and call can benefit from using multiple threads for larger datasets.
rule bcftools_call: input: fa="data/genome.fa", bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES), bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES), output: "calls/all.vcf", + threads: 4 shell: - "bcftools mpileup -f {input.fa} {input.bam} | " - "bcftools call -mv - > {output}" + "bcftools mpileup --threads {threads} -f {input.fa} {input.bam} | " + "bcftools call --threads {threads} -mv - > {output}"
1-57: Consider adding resource directives and log filesAdding resource directives and log files can help with workflow management and debugging.
For each rule, consider adding:
- Log file output
- Resources directives (memory, time)
Example for the bwa_map rule:
rule bwa_map: input: "data/genome.fa", "data/samples/{sample}.fastq", output: "mapped_reads/{sample}.bam", threads: 4 + resources: + mem_mb=8000, + runtime=60 + log: + "logs/bwa_map/{sample}.log" shell: - "bwa mem -t {threads} {input} | samtools view -Sb - > {output}" + "bwa mem -t {threads} {input} | samtools view -Sb - > {output} 2> {log}"Similar changes could be made to the other rules as well.
Would you like me to provide examples for the other rules as well?
.github/workflows/main.yml (3)
8-8: Avoid using empty branches-ignore configurationThe empty branches-ignore list will have no effect. Consider removing it or specifying branches to ignore.
pull_request: - branches-ignore: []🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
21-21: Remove trailing whitespaceThere's unnecessary trailing whitespace on this line.
- dockerfile: Dockerfile - + dockerfile: Dockerfile🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 21-21: trailing spaces
(trailing-spaces)
46-54: Upgrade checkout action and add missing newlineThe checkout action is using an older version, and the file is missing a newline at the end.
test: runs-on: ubuntu-latest needs: docker-build steps: - name: Checkout Code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Run Tests - run: docker run snakemake-tutorial snakemake --cores 1 + run: docker run snakemake-tutorial snakemake --cores 1🧰 Tools
🪛 actionlint (1.7.4)
51-51: 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)
🪛 YAMLlint (1.35.1)
[error] 54-54: no new line character at the end of file
(new-line-at-end-of-file)
[error] 54-54: trailing spaces
(trailing-spaces)
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.github/workflows/main.yml(1 hunks).gitignore(1 hunks)workflow/Snakefile(1 hunks)workflow/scripts/plot-quals.py(1 hunks)
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`**/*.py`: Do not try to improve formatting. Do not suggest ...
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
workflow/scripts/plot-quals.py
🪛 Ruff (0.8.2)
workflow/scripts/plot-quals.py
6-6: Undefined name snakemake
(F821)
9-9: Undefined name snakemake
(F821)
🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
51-51: 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)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
[error] 21-21: trailing spaces
(trailing-spaces)
[error] 54-54: no new line character at the end of file
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[error] 54-54: trailing spaces
(trailing-spaces)
🔇 Additional comments (8)
.gitignore (1)
1-5: Appropriate configuration for Snakemake workflow outputsThe .gitignore entries correctly exclude directories that will contain generated files from the Snakemake workflow (calls, plots, sorted_reads, mapped_reads) as well as the Snakemake working directory (.snakemake).
workflow/scripts/plot-quals.py (1)
1-5: Configuration setup looks goodThe script properly sets the non-interactive Agg backend for matplotlib and imports the necessary libraries.
workflow/Snakefile (4)
1-2: LGTM: Sample definition looks goodThe SAMPLES list is correctly defined at the top of the file.
4-7: All rule correctly defines the workflow outputThe rule all properly specifies the final output file that the workflow will generate.
29-36: LGTM: Samtools index rule looks goodThe samtools_index rule is properly implemented.
50-57: LGTM: Plot quals rule is well implementedThe plot_quals rule correctly uses the script to generate a quality score plot.
.github/workflows/main.yml (2)
11-24: Docker build job looks goodThe docker-build job correctly sets up checkout, linting, and image building steps.
🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
[error] 21-21: trailing spaces
(trailing-spaces)
25-45: Lint job is well configuredThe lint job is set up correctly with proper dependencies and steps.
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Actionable comments posted: 1
🧹 Nitpick comments (4)
.github/workflows/main.yml (4)
7-9: Empty 'branches-ignore' Field.
The "branches-ignore" field is set to an empty list, which actionlint flags as an issue. If you do not intend to ignore any branches, consider removing this field altogether, or otherwise specify the branches you want to ignore.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
14-14: Incorrect Indentation for Step Items.
YAMLLint expects step items to be indented with 2 additional spaces relative to their parent "steps:" key (i.e. 6 spaces total), but line 14 currently shows 4 spaces. Please adjust the indentation for all step items accordingly.🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
22-22: Remove Trailing Spaces.
There are trailing spaces on this line (line 22) that violate YAML lint rules. Please remove the extra whitespace to ensure consistent formatting.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 22-22: trailing spaces
(trailing-spaces)
55-55: Ensure Proper File Ending.
Line 55 contains trailing spaces and is missing a newline at the end of the file. Please remove the trailing spaces and add a newline to adhere to YAML best practices.- - name: Run Tests - run: docker run snakemake-tutorial snakemake --cores 1 + - name: Run Tests + run: docker run snakemake-tutorial snakemake --cores 1🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 55-55: no new line character at the end of file
(new-line-at-end-of-file)
[error] 55-55: trailing spaces
(trailing-spaces)
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🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
52-52: 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)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 55-55: no new line character at the end of file
(new-line-at-end-of-file)
[error] 55-55: trailing spaces
(trailing-spaces)
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🧹 Nitpick comments (4)
.github/workflows/main.yml (4)
8-8: Revisit the 'branches-ignore' Setting
Thebranches-ignorefield on line 8 is currently set to an empty list. If there is no branch to ignore, consider removing this field to avoid confusion; otherwise, populate it with the appropriate branch names.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
14-14: Correct YAML List Item Indentation
Line 14 (the beginning of the "Checkout Code" step) is indented with 4 spaces, but YAML best practices would typically expect 6 spaces for list entries under thestepskey. Please update the indentation as shown below:- - name: Checkout Code + - name: Checkout Code🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
22-22: Remove Trailing Spaces
There are trailing spaces detected on line 22. Removing these unnecessary spaces will help keep the YAML file clean and prevent potential linting issues.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 22-22: trailing spaces
(trailing-spaces)
55-55: Fix File Termination Formatting
Line 55 ends with trailing spaces and is missing the newline character at the end of the file. Please update the file so that it ends with a clean newline and without extra spaces.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 55-55: no new line character at the end of file
(new-line-at-end-of-file)
[error] 55-55: trailing spaces
(trailing-spaces)
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.github/workflows/main.yml(1 hunks)
🧰 Additional context used
🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 55-55: no new line character at the end of file
(new-line-at-end-of-file)
[error] 55-55: trailing spaces
(trailing-spaces)
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Actionable comments posted: 2
🧹 Nitpick comments (4)
.github/workflows/main.yml (4)
7-8: Review thebranches-ignoreSetting.
The pull_request trigger currently specifiesbranches-ignore: [], which is effectively redundant. Consider removing this key or populating it with the intended branch patterns to ignore.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
25-25: Remove Trailing Spaces on Line 25.
Trailing whitespace detected on this line. Removing such extraneous spaces will improve readability and prevent potential YAML lint warnings.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 25-25: trailing spaces
(trailing-spaces)
36-36: Remove Trailing Spaces on Line 36.
There are unnecessary trailing spaces on this line. Please remove them to adhere to clean YAML formatting practices.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 36-36: trailing spaces
(trailing-spaces)
91-91: Remove Trailing Spaces on Line 91.
Trailing spaces are present at the end of theRun Testscommand. Removing them will ensure consistency in formatting.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 91-91: trailing spaces
(trailing-spaces)
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🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[warning] 14-14: wrong indentation: expected 6 but found 4
(indentation)
[error] 25-25: trailing spaces
(trailing-spaces)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 91-91: trailing spaces
(trailing-spaces)
⏰ Context from checks skipped due to timeout of 90000ms (1)
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🧹 Nitpick comments (5)
.github/workflows/main.yml (5)
1-9: Workflow Naming and Trigger Configuration
The workflow name change to "Build, Lint, and Test" improves clarity. However, note that thebranches-ignorefield underpull_request(line 8) is set to an empty array. This can trigger warnings (as flagged by actionlint) and may lead to unintended behavior. Consider either removing this key if it's not needed or specifying the branches that should be ignored.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
23-28: Trailing Spaces in Dockerfile Lint Step
Trailing spaces are detected at the end of line 28. Please remove these trailing spaces to ensure the YAML passes linting without issues.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
37-42: Upload Artifact Step Review
The "Upload Artifact" step correctly uploads the Docker image tarball using the specified environment variable. However, be sure to remove any trailing spaces (for example, as flagged on line 39) to maintain clean YAML formatting.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 39-39: trailing spaces
(trailing-spaces)
76-97: Test Job Configuration and Artifact Usage
Thetestjob now depends on thedocker-buildjob and includes the following positive updates:
- It checks out the code using the updated
actions/checkout@v4and sets up Buildx.- The steps for downloading the Docker image artifact, loading the image, and executing the tests using
snakemakeare correctly implemented.
Note: There are trailing spaces at the end of line 96. Removing these will help pass YAML linting checks.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 96-96: trailing spaces
(trailing-spaces)
96-96: Remove Trailing Spaces in Test Run Command
Trailing spaces are present at the end of line 96. Please remove these extra spaces to meet YAML formatting standards.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 96-96: trailing spaces
(trailing-spaces)
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🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
[error] 96-96: trailing spaces
(trailing-spaces)
⏰ Context from checks skipped due to timeout of 90000ms (1)
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🔇 Additional comments (3)
.github/workflows/main.yml (3)
10-12: Environment Variable Configuration
The environment variableDOCKER_TAG_NAMEis clearly defined as "snakemake-tutorial", which is consistently used across jobs. No changes needed here.
14-42: Docker-Build Job Configuration
Thedocker-buildjob is well structured. The following points are noted:
- The checkout action is updated to
actions/checkout@v4as intended.- The steps for setting up Buildx, linting the Dockerfile (using
hadolint/hadolint-action@v3.1.0), building the Docker image (with proper tagging and artifact output), and uploading the artifact are clearly defined.
Overall, the configuration is consistent and adheres to best practices.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
43-75: Lint Job Configuration
Thelintjob is correctly set up and depends on the successful completion of thedocker-buildjob. Key observations:
- It uses
actions/checkout@v4with full repository history (fetch-depth: 0), which is appropriate for linting purposes.- The Buildx setup and the linter for the Snakefile (using
github/super-linter@v7) are well-configured with the necessary environment variables.- The steps for downloading the Docker image artifact, loading the image, and performing a dry run of the Snakefile are properly implemented.
Overall, this job is well crafted.
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🧹 Nitpick comments (5)
.github/workflows/main.yml (5)
8-9: Empty 'branches-ignore' configuration.
The pull_request trigger specifiesbranches-ignore: [], which is effectively a no-op. If the intent is to trigger on all branches, consider either removing this key or adding a comment to clarify the intent.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
28-28: Remove trailing whitespace.
Trailing spaces detected on line 28 can be removed to improve YAML cleanliness.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
39-39: Remove trailing whitespace.
Trailing spaces are found on line 39. Removing these will help maintain consistent formatting.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 39-39: trailing spaces
(trailing-spaces)
64-69: Use environment variable for artifact name consistency.
While the environment variableDOCKER_TAG_NAMEis defined with the valuesnakemake-tutorial, the artifact download step hardcodes the name. For uniformity, consider replacing the hardcoded value with the env variable. For example:- name: snakemake-tutorial + name: ${{ env.DOCKER_TAG_NAME }}
98-98: Remove extra blank lines.
Static analysis indicates there is an extra blank line at the end. Removing unnecessary blank lines will help conform to style guidelines.🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 98-98: too many blank lines
(1 > 0) (empty-lines)
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🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
[warning] 98-98: too many blank lines
(1 > 0) (empty-lines)
⏰ Context from checks skipped due to timeout of 90000ms (1)
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♻️ Duplicate comments (1)
.github/workflows/main.yml (1)
97-101:⚠️ Potential issueRemove Erroneous '-tutorial' Flag in 'Run Tests' Step.
The extra-tutorialargument in the Docker run command is likely unintended and could cause command errors. Please update the command as follows:- conda run -n ${{env.DOCKER_TAG_NAME}} -tutorial snakemake --cores 1 + conda run -n ${{env.DOCKER_TAG_NAME}} snakemake --cores 1🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 101-101: too many blank lines
(1 > 0) (empty-lines)
🧹 Nitpick comments (5)
.github/workflows/main.yml (5)
8-9: Ensure Proper 'branches-ignore' Configuration.
Thebranches-ignorefield is currently set to an empty array, which may not be intended. Consider specifying branches to ignore (if any) or remove the key if not used to avoid potential confusion.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
27-28: Remove Trailing Whitespace.
Trailing spaces detected on line 28 should be removed to comply with YAML formatting standards.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
37-42: Remove Trailing Whitespace in 'Upload Artifact' Step.
Trailing spaces on line 39 should be eliminated to satisfy YAML linting requirements.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 39-39: trailing spaces
(trailing-spaces)
73-77: Clean Up 'DryRun Snakefile' Step Formatting.
Trailing whitespace is present on line 74. Please remove the extra spaces to improve maintainability and adhere to style standards.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 74-74: trailing spaces
(trailing-spaces)
101-102: Eliminate Extra Blank Line at End of File.
A warning indicates there is one extra blank line at the end of the file. Please remove it to conform with YAML formatting standards.🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 101-101: too many blank lines
(1 > 0) (empty-lines)
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.github/workflows/main.yml(1 hunks)
🧰 Additional context used
🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
[error] 74-74: trailing spaces
(trailing-spaces)
[warning] 101-101: too many blank lines
(1 > 0) (empty-lines)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: docker-build
🔇 Additional comments (1)
.github/workflows/main.yml (1)
43-61: Positive Addition: 'lint' Job.
The newlintjob that checks out code, sets up Buildx, and lints the Snakefile is a valuable addition to improve code quality.
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Actionable comments posted: 0
🧹 Nitpick comments (4)
.github/workflows/main.yml (4)
7-9: Clarify the use of an emptybranches-ignorelist.
Thebranches-ignorefield underpull_requestis currently set to an empty array. If no branches need to be ignored, consider removing this key to avoid confusion. Otherwise, update it with the intended branch names to ignore.🧰 Tools
🪛 actionlint (1.7.4)
8-8: "branches-ignore" section should not be empty
(syntax-check)
28-28: Remove Trailing Whitespace.
A static analysis tool flagged trailing spaces on this line. Removing them will help maintain clean YAML formatting.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
73-77: Clean Up Trailing Whitespace in Multi-line Command.
TheDryRun Snakefilestep has a multi-line command where static analysis noted trailing spaces (e.g., line 74). Removing these trailing spaces will improve YAML cleanliness.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 74-74: trailing spaces
(trailing-spaces)
97-101: Run Tests Command Verification & Cleanup.
TheRun Testsstep appropriately runs the tests using Docker with the built image. Additionally, note that a static analysis tool flagged an extra blank line (line 101). Please remove any unnecessary newlines at the end of the command block.🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 101-101: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
.github/workflows/main.yml(1 hunks)
🧰 Additional context used
🪛 actionlint (1.7.4)
.github/workflows/main.yml
8-8: "branches-ignore" section should not be empty
(syntax-check)
🪛 YAMLlint (1.35.1)
.github/workflows/main.yml
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
[error] 74-74: trailing spaces
(trailing-spaces)
[warning] 101-101: too many blank lines
(1 > 0) (empty-lines)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: docker-build
🔇 Additional comments (9)
.github/workflows/main.yml (9)
1-2: Workflow Name Update Confirmation.
The workflow has been renamed to "Build, Lint, and Test," which clearly reflects its new responsibilities.
10-11: Environment Variable Consistency.
The environment variableDOCKER_TAG_NAMEis clearly defined and used consistently across jobs. No issues found here.
14-42: Review of thedocker-buildJob.
Thedocker-buildjob is well-structured:
- It checks out the code using
actions/checkout@v4.- It sets up Buildx and uses
hadolintto lint the Dockerfile.- The Docker image is built with the tag from
env.DOCKER_TAG_NAMEand exported as an artifact.
Please verify that the output artifact (/tmp/${{ env.DOCKER_TAG_NAME }}.tar) is correctly consumed in downstream jobs.🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: trailing spaces
(trailing-spaces)
[error] 39-39: trailing spaces
(trailing-spaces)
43-51:lintJob: Checkout Step Validated.
The checkout step in thelintjob usesactions/checkout@v4withfetch-depth: 0, which is appropriate for full history if needed.
55-63: Linting Configuration for Snakefile.
TheLint Snakefilestep usesgithub/super-linter@v7with relevant environment variables. The configuration appears correct to ensure Snakefile standards.
64-69: Artifact Download Consistency.
The artifact downloaded in thelintjob uses the same name (snakemake-tutorial) as set by the environment variable. This consistency is good; please ensure the artifact path is correctly utilized in subsequent steps.
70-72: Docker Image Loading Step.
TheLoad Docker Imagestep in thelintjob correctly loads the artifact. No issues detected here.
78-93: Test Job Download and Setup Verification.
Thetestjob sets up by:
- Checking out code with
actions/checkout@v4.- Setting up Buildx.
- Downloading the Docker image artifact using the environment variable to ensure consistency.
The step order is logical and adheres to dependency requirements.
94-96: Docker Image Loading in Test Job.
TheLoad Docker Imagestep in thetestjob mirrors the process in thelintjob. It is correctly implemented.
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@jakevc this only requires review? I noticed it on the Hackathon project site. @johanneskoester? |
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Nice and a good idea in principle! One thing worries me though: we now have two sources of the workflow. One in the tutorial docs and one here. I think it would be cool to rather auto test the code snippets in the sphinx docs? One could use this one: https://www.sphinx-doc.org/en/master/usage/extensions/doctest.html
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Yeah I see what you mean. I guess the main goal of this PR is to make the whole tutorial maximally portable. This can be useful for individual users, as well as for teaching purposes. I have definitely rebuilt the tutorial from the documentation multiple time for this reason, could be nice to have an official location that is runnable end to end. What do you think about going the opposite direction: dynamically including snippets from this repo into the sphinx documentation? |
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The benefit of this approach is that it offloads the testing of the workflow to a more realistic/portable environment, the downside is I don't think there is a suitable sphinx extension that does this.... yet |
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Yes, I agree, that is better! |
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I think literalinclude should do the job: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-literalinclude When we align snakefiles here with the snippets that show up in the tutorial, one should be able to fully test that. |
Summary by CodeRabbit
New Features
Chores