Agent skill
nextflow-pipelines-generate-automatically
Sub-skill of nextflow-pipelines: Generate automatically (+2).
Install this agent skill to your Project
npx add-skill https://github.com/vamseeachanta/workspace-hub/tree/main/.claude/skills/_archive/science/bio-research/nextflow-pipelines/generate-automatically
SKILL.md
Generate automatically (+2)
Generate automatically
python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
The script:
- Discovers FASTQ/BAM/CRAM files
- Pairs R1/R2 reads
- Infers sample metadata
- Validates before writing
For sarek: Script prompts for tumor/normal status if not auto-detected.
Validate existing samplesheet
python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
Samplesheet formats
rnaseq:
sample,fastq_1,fastq_2,strandedness
SAMPLE1,/abs/path/R1.fq.gz,/abs/path/R2.fq.gz,auto
sarek:
patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,/abs/path/tumor_R1.fq.gz,/abs/path/tumor_R2.fq.gz,1
*See sub-skills for full details.*
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