references/default-workflows.json

{
  "schema_version": 1,
  "workflows": [
    {"workflow_id":"fastq_qc","name":"FASTQ QC","description":"Basic FASTQ quality checks with FastQC and MultiQC, with optional SeqTK trimming.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/demo","revision":"1.2.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"rnaseq","name":"Bulk RNA-seq","description":"Bulk RNA-seq FASTQ to QC, alignment or pseudoalignment, quantification, and MultiQC.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/rnaseq","revision":"3.26.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"scrnaseq","name":"Single-cell RNA-seq","description":"Single-cell or single-nucleus RNA-seq FASTQ to count matrices and QC outputs.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/scrnaseq","revision":"4.2.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"sarek","name":"DNA variant analysis","description":"DNA germline or somatic variant analysis using nf-core/sarek.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/sarek","revision":"3.10.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"atacseq","name":"ATAC-seq","description":"ATAC-seq alignment, QC, peak calling, consensus peaks, and signal outputs.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/atacseq","revision":"2.1.2"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"chipseq","name":"ChIP-seq","description":"ChIP-seq alignment, QC, peak calling, consensus peaks, and signal outputs.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/chipseq","revision":"2.1.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"cutandrun","name":"CUT&RUN / CUT&Tag","description":"CUT&RUN or CUT&Tag alignment, QC, peak calling, and reporting.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/cutandrun","revision":"3.2.2"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"ampliseq","name":"Amplicon sequencing","description":"Marker-gene amplicon denoising, taxonomy, diversity, and reporting.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/ampliseq","revision":"2.18.0"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"taxprofiler","name":"Taxonomic profiling","description":"Shotgun metagenomics taxonomic and optional functional profiling.","engine":"nextflow","collection":"nf-core","source":{"kind":"remote","workflow":"nf-core/taxprofiler","revision":"2.0.1"},"execution":{"parameter_contract":"nf-core"}},
    {"workflow_id":"oai_fastq_qc","name":"Bundled FASTQ QC","description":"Bundled FastQC, optional trimming, and MultiQC workflow.","engine":"snakemake","collection":"OpenAI","source":{"kind":"local","root":"workflows/fastq_qc","entrypoint":"workflow/Snakefile"},"execution":{"default_config":"config/config.json"}},
    {"workflow_id":"oai_bulk_rnaseq_counts_qc","name":"Bundled bulk RNA-seq","description":"Bundled FastQC, Salmon quantification, matrix aggregation, and MultiQC workflow.","engine":"snakemake","collection":"OpenAI","source":{"kind":"local","root":"workflows/bulk_rnaseq_counts_qc","entrypoint":"workflow/Snakefile"},"execution":{"default_config":"config/config.json"}},
    {"workflow_id":"oai_scrnaseq_fastq_to_count","name":"Bundled single-cell RNA-seq","description":"Bundled STARsolo FASTQ-to-count workflow.","engine":"snakemake","collection":"OpenAI","source":{"kind":"local","root":"workflows/scrnaseq_fastq_to_count","entrypoint":"workflow/Snakefile"},"execution":{"default_config":"config/config.json"}}
  ]
}