nascent_outputs.md

Workflow outputs migration: nascent

• Generated: 2026-07-17T00:30:21.814001+00:00
• Status: ❌ error — no output {} block found; still relies on the legacy publishDir directive

This report tracks migration from the legacy publishDir directive to the new workflow outputs syntax.

Workflow output {} blocks

No top-level output {} block found. See the docs for how to add one: https://docs.seqera.io/nextflow/tutorials/workflow-outputs

Legacy publishDir references

Found 42 publishDir references across 7 files that should be migrated to the workflow output {} block:

• conf/modules.config — 36 references
• modules/nf-core/rseqc/bamstat/tests/nextflow.config — 1 reference
• modules/nf-core/rseqc/inferexperiment/tests/nextflow.config — 1 reference
• modules/nf-core/rseqc/innerdistance/tests/nextflow.config — 1 reference
• modules/nf-core/subread/featurecounts/tests/nextflow.config — 1 reference
• subworkflows/nf-core/fastq_align_star/tests/nextflow.config — 1 reference
• subworkflows/nf-core/fastq_align_star/tests/with_transcripts.config — 1 reference