Sub-skill of nextflow-pipelines: Check completion (+1).
Scanned 9/9/2026
Install to Claude Code
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---
name: nextflow-pipelines-check-completion
description: 'Sub-skill of nextflow-pipelines: Check completion (+1).'
version: 1.0.0
category: science
type: reference
scripts_exempt: true
---
# 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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