nextflow-development
Prepare nf-core samplesheets, cluster nextflow.config, and write launch artifacts. nfcore_launch.py only wraps nf-core/rnaseq and nf-core/scrnaseq with optional nextflow -preview. Other pipelines still use generate_samplesheet.py plus a hand-written nextflow run. Does not reimplement the pipelines.
Pinned to revision 683018420a75, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/nextflow-development/SKILL.md
- skills/nextflow-development/LICENSE.txt
- skills/nextflow-development/references/geo-sra-acquisition.md
- skills/nextflow-development/references/installation.md
- skills/nextflow-development/references/pipelines/atacseq.md
- skills/nextflow-development/references/pipelines/rnaseq.md
- skills/nextflow-development/references/pipelines/sarek.md
- skills/nextflow-development/references/troubleshooting.md
- skills/nextflow-development/scripts/check_environment.py
- skills/nextflow-development/scripts/cluster_profile_generator.py
- skills/nextflow-development/scripts/config/genomes.yaml
- skills/nextflow-development/scripts/config/pipelines/atacseq.yaml
- skills/nextflow-development/scripts/config/pipelines/methylseq.yaml
- skills/nextflow-development/scripts/config/pipelines/nanoseq.yaml
- skills/nextflow-development/scripts/config/pipelines/proteinfold.yaml
- skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml
- skills/nextflow-development/scripts/config/pipelines/sarek.yaml
- skills/nextflow-development/scripts/config/pipelines/scrnaseq.yaml
- skills/nextflow-development/scripts/detect_data_type.py
- skills/nextflow-development/scripts/generate_samplesheet.py
- skills/nextflow-development/scripts/manage_genomes.py
- skills/nextflow-development/scripts/nfcore_launch.py
- skills/nextflow-development/scripts/sra_geo_fetch.py
- skills/nextflow-development/scripts/utils/__init__.py
- skills/nextflow-development/scripts/utils/file_discovery.py
- skills/nextflow-development/scripts/utils/ncbi_utils.py
- skills/nextflow-development/scripts/utils/sample_inference.py
- skills/nextflow-development/scripts/utils/validators.py
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