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nf-core-pipelines

separate

Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and selecting a container engine and institutional config via -profile. Use when deciding to adopt a community pipeline versus author one from scratch; picking a pipeline and pinning its -r revision; selecting -profile test/docker/singularity/conda plus an institutional config from nf-core/configs; building and validating a samplesheet CSV against the pipeline schema (nf-schema); choosing --genome/iGenomes versus custom references; configuring resources and max_memory for SLURM/AWS Batch; using -resume and -stub; and reading MultiQC outputs.

When to use

• adopting community pipelines
• pinning pipeline revisions
• selecting container profiles
• validating samplesheets
• configuring references
• configuring resources
• using resume and stub
• reading MultiQC outputs

When not to use

• authoring pipelines from scratch
• one-off linear steps
• single sample single machine tasks

Skill page

Source