# Nextflow Pipelines Check Completion

> Sub-skill of nextflow-pipelines: Check completion (+1).

- Skill: `vamseeachanta/nextflow-pipelines-check-completion` (Agent Skill)
- Install (CLI): `npx skillmds@latest add vamseeachanta/nextflow-pipelines-check-completion`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vamseeachanta/nextflow-pipelines-check-completion/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Research & Search
- Author: vamseeachanta (https://skillmd.com/u/vamseeachanta)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/vamseeachanta/nextflow-pipelines-check-completion

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# Check completion (+1)

## Check completion


```bash
ls results/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log
```

## Key outputs by pipeline


**rnaseq:**
- `results/star_salmon/salmon.merged.gene_counts.tsv` - Gene counts
- `results/star_salmon/salmon.merged.gene_tpm.tsv` - TPM values

**sarek:**
- `results/variant_calling/*/` - VCF files
- `results/preprocessing/recalibrated/` - BAM files

**atacseq:**
- `results/macs2/narrowPeak/` - Peak calls
- `results/bwa/mergedLibrary/bigwig/` - Coverage tracks

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