Add SAMTOOLS_INDEX process to sample tracking workflow#10
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nvnieuwk merged 13 commits intonf-cmgg:devfrom Aug 11, 2025
Merged
Add SAMTOOLS_INDEX process to sample tracking workflow#10nvnieuwk merged 13 commits intonf-cmgg:devfrom
nvnieuwk merged 13 commits intonf-cmgg:devfrom
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Very good! I have some small suggestion mainly to nitpick and keep good code practices but the data flow is exactly how it should be 🥳
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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
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Can you remove the BWA index from the code?
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| params { | ||
| input = "${projectDir}/assets/samplesheet.csv" | ||
| bwa_index = "s3://test-data/genomics/homo_sapiens/genome/bwa/" | ||
| bwa_index = "/mnt/c/Users/sampletracking/bwa" |
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| bwa_index = "/mnt/c/Users/sampletracking/bwa" | |
| bwa_index = "s3://test-data/genomics/homo_sapiens/genome/bwa/" |
Please revert this back to the S3 URL
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Introduce a new process for indexing SAM/BAM/CRAM files within the sample tracking workflow, enhancing data management capabilities. This includes necessary configurations and tests for the new process.