Nextflow Pipelines Check Completion

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

vamseeachanta Updated

File contents

Check completion (+1)

Check completion

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

vamseeachanta/workspace-hub/tree/main/.agents/skills/_archive/science/bio-research/nextflow-pipelines/check-completion commit 4793863e38

Frequently asked questions

npx skillmds@latest add vamseeachanta/nextflow-pipelines-check-completion