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Recipes

20 recipes, each invokable as bioflow recipe run <name> [options]. Auto-generated from the recipe registry by scripts/gen_docs.py.

amr_vf_catalogue

ABRicate × N genomes × M databases (AMR + VF + plasmid)

1 stage(s):

  • abricate_one — staphb/abricate:1.4.0

ani_matrix

All-vs-all ANI matrix (FastANI 1.34)

1 stage(s):

  • fastani_all_vs_all — staphb/fastani:1.34

atac_seq

ATAC-seq: TrimGalore → Bowtie2 → Picard → MACS3 → TOBIAS

5 stage(s):

  • trim — quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0
  • align — staphb/bowtie2:2.5.5
  • dedup — quay.io/biocontainers/picard:3.4.0--hdfd78af_0
  • call_peaks — quay.io/biocontainers/macs3:3.0.4--py310h5a5e57a_0
  • footprint — quay.io/biocontainers/tobias:0.17.3--py39hff726c5_1

cafe_evolution

Gene family expansion/contraction (CAFE5)

1 stage(s):

  • run_cafe5 — quay.io/biocontainers/cafe:5.1.0--h5ca1c30_1

chip_seq

ChIP-seq: TrimGalore → Bowtie2 → Picard → MACS3 → HOMER

5 stage(s):

  • trim — quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0
  • align — staphb/bowtie2:2.5.5
  • dedup — quay.io/biocontainers/picard:3.4.0--hdfd78af_0
  • call_peaks — quay.io/biocontainers/macs3:3.0.4--py310h5a5e57a_0
  • annotate_peaks — quay.io/biocontainers/homer:5.1--pl5321hc52dbad_1

cog_enrichment

Pangenome × COG-2024 functional-category enrichment

2 stage(s):

  • diamond_makedb — quay.io/biocontainers/diamond:2.2.2--he361c42_0
  • diamond_blastp — quay.io/biocontainers/diamond:2.2.2--he361c42_0

download_taxon

Download every RefSeq assembly for a taxon (no Docker)

0 stage(s):

eukaryote_assembly

Eukaryote long-read assembly: NanoPlot → Flye → Medaka → compleasm

4 stage(s):

  • read_qc — quay.io/biocontainers/nanoplot:1.47.1--pyhdfd78af_0
  • assemble — quay.io/biocontainers/flye:2.9.6--py313h7fbb527_1
  • polish_consensus — quay.io/biocontainers/medaka:2.2.2--py312h3050eb1_0
  • assess — quay.io/biocontainers/compleasm:0.2.8--pyh106432d_0

germline_variants

Germline variants: fastp → BWA → GATK → bcftools → SnpEff

6 stage(s):

  • prepare_reference — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
  • qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • align — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
  • call_variants — quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1
  • filter_variants — quay.io/biocontainers/bcftools:1.23.1--hb2cee57_0
  • annotate_variants — quay.io/biocontainers/snpeff:5.4.0c--hdfd78af_0

gwas

Scoary GWAS over a Roary pangenome

1 stage(s):

  • run_scoary — quay.io/biocontainers/scoary:1.6.16--py_2

joint_genotyping

Cohort joint genotyping (GATK best practice): per-sample GVCF → CombineGVCFs → GenotypeGVCFs → hard-filter → SnpEff

8 stage(s):

  • prepare_reference — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
  • qc_one — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • align_one — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
  • call_gvcf — quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1
  • combine_gvcfs — quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1
  • genotype_cohort — quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1
  • hard_filter — quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1
  • annotate_cohort — quay.io/biocontainers/snpeff:5.4.0c--hdfd78af_0

metagenome_assembly

Metagenome assembly + binning: fastp → MEGAHIT → minimap2 → MetaBAT2 → CheckM2

5 stage(s):

  • qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • assemble — quay.io/biocontainers/megahit:1.2.9--h2e03b76_1
  • map_back — quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:b411340b52d82a9c276d87c7a3dcffc880be762f-0
  • bin_genomes — quay.io/biocontainers/metabat2:2.18--h38e344b_2
  • assess_bins — quay.io/biocontainers/checkm2:1.1.0--pyh7e72e81_1

metagenomics_profile

Shotgun metagenomic profiling: fastp → Kraken2 → Bracken → Krona

4 stage(s):

  • qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • kraken2_classify — quay.io/biocontainers/kraken2:2.1.6--pl5321h077b44d_0
  • bracken_abundance — quay.io/biocontainers/bracken:3.1--h9948957_0
  • krona_chart — staphb/krona:2.8.1

methylation_wgbs

WGBS methylation: TrimGalore → Bismark → methylKit

4 stage(s):

  • bismark_prep — quay.io/biocontainers/bismark:0.25.1--hdfd78af_0
  • trim — quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0
  • bismark_align — quay.io/biocontainers/bismark:0.25.1--hdfd78af_0
  • methylkit_dmr — quay.io/biocontainers/bioconductor-methylkit:1.36.0--r45ha27e39d_0

pangenome

Pangenome from a taxon: NCBI fetch → parallel Prokka → Roary

2 stage(s):

  • annotate — staphb/prokka:1.14.6
  • run_roary — staphb/roary:3.13.0

phylogeny

Single-copy core gene supermatrix → MAFFT × N → IQ-TREE ML

2 stage(s):

  • mafft_one — staphb/mafft:7.526
  • run_iqtree — staphb/iqtree2:2.4.0

prokaryote_assembly

Prokaryote short-read de novo assembly + Prokka annotation

6 stage(s):

  • qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • assemble — staphb/spades:4.2.0
  • annotate — staphb/prokka:1.14.6
  • assembly_qc — staphb/quast:5.3.0
  • genome_plot — staphb/genovi:0.4.3
  • graph_image — staphb/bandage:0.9.0

proteomics_dda

LC-MS/MS DDA proteomics: msconvert → Comet → Percolator

3 stage(s):

  • msconvert — chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:latest
  • comet_search — quay.io/biocontainers/comet-ms:2026011--h9ee0642_0
  • percolator_fdr — quay.io/biocontainers/percolator:3.9--h0f90025_0

rnaseq_deg

RNA-seq DEG: fastp → Salmon → DESeq2 → GO enrichment + MultiQC

6 stage(s):

  • multiqc_report — quay.io/biocontainers/multiqc:1.35--pyhdfd78af_1
  • qc_one — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  • salmon_index — quay.io/biocontainers/salmon:2.3.1--hfa8f182_0
  • salmon_quant — quay.io/biocontainers/salmon:2.3.1--hfa8f182_0
  • deseq2_diff — quay.io/biocontainers/bioconductor-deseq2:1.50.2--r45ha27e39d_0
  • enrich_go — quay.io/biocontainers/gseapy:1.3.0--py311heb3b1e3_0

scrna_seq

scRNA-seq (10x): STARsolo + Scanpy QC/cluster/UMAP

2 stage(s):

  • starsolo — quay.io/biocontainers/star:2.7.11b--h43eeafb_0
  • scanpy_analyze — ghcr.io/hope9901/bioflow-scanpy:1.12.2