docs: paper #111
docs: paper #111
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WalkthroughA new document titled "A Snakemake workflow for differential expression analysis with alternative splicing detection using long read data" has been added. The document details a modular, reproducible workflow optimized for high-performance computing environments. It outlines steps including quality filtering, read alignment, quantification, differential expression analysis, and alternative splicing detection using a modified FLAIR toolkit. An optional annotation procedure for under-annotated or novel genomes is also described. Additionally, a new GitHub Actions workflow has been introduced to automate the generation and upload of a draft PDF from the document. Changes
Sequence Diagram(s)sequenceDiagram
participant User as User/HPC
participant Workflow as Snakemake Workflow
participant Quality as Quality Filtering
participant Align as Read Alignment
participant Quant as Quantification
participant DiffExp as Differential Analysis
participant Splice as Splicing Analysis (FLAIR)
participant Annot as Optional Annotation
User->>Workflow: Start workflow with input data
Workflow->>Quality: Execute quality filtering
Quality-->>Workflow: Return filtered data
Workflow->>Align: Perform read alignment
Align-->>Workflow: Return aligned reads
Workflow->>Quant: Quantify transcripts
Quant-->>Workflow: Return expression data
Workflow->>DiffExp: Run differential expression analysis
DiffExp-->>Workflow: Return statistical outcomes
Workflow->>Splice: Perform splicing analysis using FLAIR
Splice-->>Workflow: Return isoform data
Workflow->>Annot: (Optional) Annotate novel genomes
Annot-->>Workflow: Return annotation details
Workflow-->>User: Provide final workflow output
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Actionable comments posted: 1
🧹 Nitpick comments (7)
paper/paper.md (7)
4-10: Correct Typos in Title and Tags
The title and the tags contain typographical errors. In the title, "analyis" should be corrected to "analysis" and in the tags, "alterternative splicing detection" should be corrected to "alternative splicing detection".-title: 'A Snakemake workflow for differential expression analyis with alternative splicing detection using long read data' +title: 'A Snakemake workflow for differential expression analysis with alternative splicing detection using long read data' - - alterternative splicing detection + - alternative splicing detection🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
6-6: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
7-7: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
8-8: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
9-9: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
10-10: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
19-20: Review Placeholder ORCID Value
The ORCID for Christiane Krämer is set as "XXX ?". If this is a placeholder, please update it with a valid ORCID or remove the placeholder to maintain professionalism.
31-31: Remove Inline Comment from Date Field
The date field includes the annotation " <- update". Consider removing this inline note before finalizing the document to ensure the metadata remains clean.
5-10: Address YAML List Indentation Issues in Tags Block
Markdownlint has flagged unordered list indentation issues (MD007) for the tags block. You might either adjust the indentation to conform to the linter’s expectations or configure the linter to ignore YAML front matter.🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
6-6: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
7-7: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
8-8: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
9-9: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
10-10: Unordered list indentation
Expected: 0; Actual: 2(MD007, ul-indent)
25-29: Ensure Consistent Indentation in Affiliations Block
There are inconsistent indentation issues in the affiliations list. Align the list items and their sub-properties uniformly to improve readability and prevent potential parsing issues.🧰 Tools
🪛 LanguageTool
[uncategorized] ~28-~28: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...ny index: 1 - name: NHR-SouthWest / High Performance Computing Group, Johannes Gutenberg-Uni...(EN_COMPOUND_ADJECTIVE_INTERNAL)
🪛 markdownlint-cli2 (0.17.2)
26-26: Inconsistent indentation for list items at the same level
Expected: 2; Actual: 1(MD005, list-indent)
26-26: Unordered list indentation
Expected: 0; Actual: 1(MD007, ul-indent)
28-28: Inconsistent indentation for list items at the same level
Expected: 2; Actual: 1(MD005, list-indent)
28-28: Unordered list indentation
Expected: 0; Actual: 1(MD007, ul-indent)
78-78: Fix Typo and Enhance Readability in Quality Filtering Section
The word "Prioar" appears to be a typo and should be corrected to "Prior to". Additionally, consider inserting a comma after the introductory phrase "For this" to improve clarity (i.e. "For this, we make use of the BioPython library...").🧰 Tools
🪛 LanguageTool
[typographical] ~78-~78: Use a comma after an introductory phrase.
Context: ...ead quality and read length thresholds. For this we make use of the BioPython library [@...(COMMA_INTRODUCTORY_WORDS_PHRASES)
93-93: Remove Placeholder Text for Rulegraph
The text "ADD rulegraph and caption, here." appears to be a placeholder. Ensure that this placeholder is replaced with the final rulegraph content or removed before merging the draft paper.
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paper/paper.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
paper/paper.md
[uncategorized] ~28-~28: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...ny index: 1 - name: NHR-SouthWest / High Performance Computing Group, Johannes Gutenberg-Uni...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[typographical] ~78-~78: Use a comma after an introductory phrase.
Context: ...ead quality and read length thresholds. For this we make use of the BioPython library [@...
(COMMA_INTRODUCTORY_WORDS_PHRASES)
🪛 markdownlint-cli2 (0.17.2)
paper/paper.md
6-6: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
7-7: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
8-8: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
9-9: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
10-10: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
12-12: Unordered list indentation
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(MD007, ul-indent)
15-15: Unordered list indentation
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(MD007, ul-indent)
18-18: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
21-21: Unordered list indentation
Expected: 0; Actual: 2
(MD007, ul-indent)
26-26: Inconsistent indentation for list items at the same level
Expected: 2; Actual: 1
(MD005, list-indent)
26-26: Unordered list indentation
Expected: 0; Actual: 1
(MD007, ul-indent)
28-28: Inconsistent indentation for list items at the same level
Expected: 2; Actual: 1
(MD005, list-indent)
28-28: Unordered list indentation
Expected: 0; Actual: 1
(MD007, ul-indent)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Testing
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Actionable comments posted: 3
🧹 Nitpick comments (1)
.github/workflows/draft-pdf.yml (1)
28-28: Newline at End of FileThe linter also reported that there’s no newline character at the end of the file (line 28). Please add a newline to adhere to best practices and avoid potential issues in some tools.
🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 28-28: no new line character at the end of file
(new-line-at-end-of-file)
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📒 Files selected for processing (1)
.github/workflows/draft-pdf.yml(1 hunks)
🧰 Additional context used
🪛 YAMLlint (1.35.1)
.github/workflows/draft-pdf.yml
[warning] 4-4: wrong indentation: expected 8 but found 6
(indentation)
[warning] 5-5: wrong indentation: expected 10 but found 8
(indentation)
[warning] 9-9: wrong indentation: expected 4 but found 2
(indentation)
[warning] 10-10: wrong indentation: expected 6 but found 4
(indentation)
[warning] 13-13: wrong indentation: expected 8 but found 6
(indentation)
[warning] 18-18: wrong indentation: expected 12 but found 10
(indentation)
[warning] 24-24: wrong indentation: expected 12 but found 10
(indentation)
[error] 28-28: no new line character at the end of file
(new-line-at-end-of-file)
| jobs: | ||
| paper: | ||
| runs-on: ubuntu-latest | ||
| name: Paper Draft | ||
| steps: |
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🛠️ Refactor suggestion
Jobs Block: Correct Indentation
The jobs section also shows inconsistent indentation. For instance, line 9 (the key paper:) is indented with 2 spaces while the expected indentation is 4, and line 10’s runs-on: ubuntu-latest should be indented by 6 spaces rather than 4.
A consistent reindentation might look like this:
Adjust the rest of the document similarly to maintain uniformity.
Committable suggestion skipped: line range outside the PR's diff.
🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 9-9: wrong indentation: expected 4 but found 2
(indentation)
[warning] 10-10: wrong indentation: expected 6 but found 4
(indentation)
.github/workflows/draft-pdf.yml
Outdated
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| - name: Build draft PDF | ||
| uses: openjournals/openjournals-draft-action@master | ||
| with: | ||
| journal: joss | ||
| # This should be the path to the paper within your repo. | ||
| paper-path: paper/paper.md | ||
| - name: Upload | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: paper | ||
| # This is the output path where Pandoc will write the compiled | ||
| # PDF. Note, this should be the same directory as the input | ||
| # paper.md |
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🛠️ Refactor suggestion
Steps Block: Reindent Step Items and Parameters
Several steps within the job have indentation issues as well. Static analysis reports that:
- Line 13 (“- name: Checkout”) is indented with 6 spaces instead of the expected 8.
- Line 18 (the “journal: joss” key) is indented with 10 spaces when 12 are expected.
- Line 24 (“name: paper”) similarly shows too few spaces.
A suggested reindentation for the steps block using a 2-space-per-level standard is:
This will help clear the YAML lint warnings and ensure that the workflow is parsed correctly.
Committable suggestion skipped: line range outside the PR's diff.
🧰 Tools
🪛 YAMLlint (1.35.1)
[warning] 13-13: wrong indentation: expected 8 but found 6
(indentation)
[warning] 18-18: wrong indentation: expected 12 but found 10
(indentation)
[warning] 24-24: wrong indentation: expected 12 but found 10
(indentation)
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🧹 Nitpick comments (4)
paper/paper.md (4)
1-31: Fix Typos and Remove Editorial Notes in Front Matter
- Line 2: The title contains a typo—“differential expression analyis” should be “differential expression analysis.”
- Line 8: The tag “alterternative splicing detection” should be corrected to “alternative splicing detection.”
- Line 29: Remove the “<- update” note from the date field once the paper’s metadata is finalized.
16-18: Review Placeholder ORCID FieldThe ORCID for Christiane Krämer is listed as
XXX ?, which appears to be a placeholder. Please update this field with the correct ORCID or remove it if not applicable.
76-77: Correct Typographical Error in Quality Filtering SectionThe sentence beginning on line 76 starts with “Prioar downstream analysis...”. It should read “Prior to downstream analysis...” to ensure clarity and correctness.
90-90: Remove Placeholder TextThe placeholder text “ADD rulegraph and caption, here.” on line 90 should be replaced with the actual rulegraph and appropriate caption, or removed if it is not required in the final draft.
🧰 Tools
🪛 LanguageTool
[uncategorized] ~90-~90: The grammatical number of this noun doesn’t look right. Consider replacing it.
Context: ...exploratory studies. ADD rulegraph and caption, here. # Usage # Acknowledgements A...(AI_EN_LECTOR_REPLACEMENT_NOUN_NUMBER)
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📒 Files selected for processing (2)
.github/workflows/draft-pdf.yml(1 hunks)paper/paper.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
paper/paper.md
[typographical] ~75-~75: Use a comma after an introductory phrase.
Context: ...ead quality and read length thresholds. For this we make use of the BioPython library [@...
(COMMA_INTRODUCTORY_WORDS_PHRASES)
[uncategorized] ~90-~90: The grammatical number of this noun doesn’t look right. Consider replacing it.
Context: ...exploratory studies. ADD rulegraph and caption, here. # Usage # Acknowledgements A...
(AI_EN_LECTOR_REPLACEMENT_NOUN_NUMBER)
🪛 YAMLlint (1.35.1)
.github/workflows/draft-pdf.yml
[error] 24-24: no new line character at the end of file
(new-line-at-end-of-file)
🔇 Additional comments (2)
.github/workflows/draft-pdf.yml (2)
1-7: YAML Trigger Configuration Looks CorrectThe trigger block under
on:is well structured using consistent 2-space indentation for keys and 6-space indentation for list items. This update resolves the previous indentation issues flagged in earlier commits.
8-24: Append Newline at End of FileStatic analysis has flagged that there is no newline character at the end of the file (line 24). Please ensure a newline is added to meet YAML formatting best practices.
🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 24-24: no new line character at the end of file
(new-line-at-end-of-file)
this PR is not to be merged until after the paper review.
The intention is to develop a paper draft together .
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Documentation
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