feat: split get_reads in two rules #125
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…plitting bam into fastqs
WalkthroughA new Snakemake rule, Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Snakemake
participant get_bams
participant get_reads
User->>Snakemake: Trigger workflow
Snakemake->>get_bams: Download BAM file from URL
get_bams->>Snakemake: BAM file saved locally
Snakemake->>get_reads: Process local BAM file to extract reads
get_reads->>Snakemake: Reads extracted
Poem
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Actionable comments posted: 0
🧹 Nitpick comments (1)
workflow/rules/download.smk (1)
1-15: Well-structured new rule for downloading BAM files.The new
get_bamsrule looks good and follows Snakemake best practices. It:
- Properly outputs to a consistent location in
resources/bams/- Uses parameters to get the BAM URL dynamically
- Includes appropriate logging
- Sets a reasonable thread count (32) for concurrent downloads
- Includes retry logic (3 attempts) which is essential for handling network issues
- Uses curl for downloading, with proper output redirection
One potential improvement would be to add validation of the downloaded file:
rule get_bams: output: bam="resources/bams/{benchmark}.bam", params: bam_url=get_benchmark_bam_url, log: "logs/download-bams/{benchmark}.log", conda: "../envs/tools.yaml" resources: sort_threads=lambda _, threads: max(threads - 2, 1), threads: 32 retries: 3 shell: - "curl {params.bam_url} --output {output.bam} 2> {log}" + "(curl {params.bam_url} --output {output.bam} && samtools quickcheck {output.bam}) 2> {log}"
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🔇 Additional comments (1)
workflow/rules/download.smk (1)
18-38: Cleanly refactored read extraction rule.The modifications to the
get_readsrule are logically correct and complete the separation of concerns between downloading BAM files and extracting reads:
- Now properly takes the downloaded BAM file as input
- Log file path has been appropriately renamed to
split-into-readsto reflect its current purpose- Shell command correctly uses the input BAM file instead of downloading from URL
- Removed the retry logic as it's no longer needed (handled by upstream rule)
The changes improve the workflow by:
- Making each step more focused and easier to debug
- Avoiding redundant downloads if extraction fails
- Allowing for clearer monitoring of each process
famosab
changed the title
|
Closed in favor of #126 |
Separate download of bam file and splitting the bam into reads in two rules.
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