Recipes¶

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

Swappable stages (`--set`)¶

Each recipe runs a recommended default tool per stage (shown in bold), overridable with --set <flag>=<tool>. For full per-stage tool choice, bioflow custom <pipeline> offers every applicable registry tool.

Recipe	Flag	Options
`atac_seq`	`--set aligner=…`	bowtie2 \| bwa
`chip_seq`	`--set aligner=…`	bowtie2 \| bwa
`eukaryote_assembly`	`--set assembler=…`	flye \| hifiasm
`germline_variants`	`--set caller=…`	deepvariant \| gatk4
`joint_genotyping`	`--set caller=…`	deepvariant \| gatk4
`metagenome_assembly`	`--set binner=…`	maxbin2 \| metabat2
`metagenomics_profile`	`--set profiler=…`	kraken2 \| metaphlan
`methylation_wgbs`	`--set aligner=…`	bowtie2 \| hisat2
`prokaryote_assembly`	`--set annotator=…`	bakta \| prokka
`proteomics_dda`	`--set search=…`	comet \| msgf
`rnaseq_deg`	`--set quantifier=…`	kallisto \| salmon
`scrna_seq`	`--set counter=…`	kb \| starsolo

`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/BWA → Picard → MACS3 → TOBIAS

Swappable: --set aligner=bowtie2 | bwa (default bowtie2).

6 stage(s):

trim — quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0
align — staphb/bowtie2:2.5.1
align_bwa — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
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/BWA → Picard → MACS3 → HOMER

Swappable: --set aligner=bowtie2 | bwa (default bowtie2).

6 stage(s):

trim — quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0
align — staphb/bowtie2:2.5.1
align_bwa — quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0
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/hifiasm → Medaka → compleasm

Swappable: --set assembler=flye | hifiasm (default flye).

5 stage(s):

read_qc — quay.io/biocontainers/nanoplot:1.47.1--pyhdfd78af_0
assemble — quay.io/biocontainers/flye:2.9.6--py313h7fbb527_1
assemble_hifiasm — quay.io/biocontainers/hifiasm:0.25.0--h5ca1c30_0
polish_consensus — quay.io/biocontainers/medaka:2.2.2--py312h3050eb1_0
assess — quay.io/biocontainers/compleasm:0.2.9--pyhdfd78af_0

`germline_variants`¶

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

Swappable: --set caller=deepvariant | gatk4 (default gatk4).

7 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
call_variants_deepvariant — google/deepvariant:1.10.0
filter_variants — quay.io/biocontainers/bcftools:1.24--h487d631_1
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/GLnexus → hard-filter → SnpEff

Swappable: --set caller=deepvariant | gatk4 (default gatk4).

11 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
call_gvcf_deepvariant — google/deepvariant:1.10.0
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
joint_call_glnexus — quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0
glnexus_to_vcf — quay.io/biocontainers/bcftools:1.24--h487d631_1

`metagenome_assembly`¶

Metagenome assembly + binning: fastp → MEGAHIT → MetaBAT2/MaxBin2 → CheckM2

Swappable: --set binner=maxbin2 | metabat2 (default metabat2).

6 stage(s):

qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
assemble — quay.io/biocontainers/megahit:1.2.9--h2e03b76_1
bin_genomes_maxbin2 — quay.io/biocontainers/maxbin2:2.2.7--h503566f_8
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|MetaPhlAn → Krona

Swappable: --set profiler=kraken2 | metaphlan (default kraken2).

5 stage(s):

qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
kraken2_classify — quay.io/biocontainers/kraken2:2.17.1--pl5321h077b44d_0
bracken_abundance — quay.io/biocontainers/bracken:3.1--h9948957_0
krona_chart — staphb/krona:2.8.1
metaphlan_profile — quay.io/biocontainers/metaphlan:4.2.4--pyhdfd78af_0

`methylation_wgbs`¶

WGBS methylation: TrimGalore → Bismark → methylKit

Swappable: --set aligner=bowtie2 | hisat2 (default bowtie2).

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 + structural annotation

Swappable: --set annotator=bakta | prokka (default prokka).

7 stage(s):

qc_trim — quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
assemble — staphb/spades:4.3.0
annotate — staphb/prokka:1.14.6
annotate_bakta — quay.io/biocontainers/bakta:1.12.0--pyhdfd78af_0
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/MS-GF+ → FDR

Swappable: --set search=comet | msgf (default comet).

5 stage(s):

msconvert — chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:latest
comet_search — quay.io/biocontainers/comet-ms:2026011--h9ee0642_0
msgf_search — quay.io/biocontainers/msgf_plus:2024.03.26--hdfd78af_0
msgf_fdr — quay.io/biocontainers/msgf_plus:2024.03.26--hdfd78af_0
percolator_fdr — quay.io/biocontainers/percolator:3.9--h0f90025_0

`rnaseq_deg`¶

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

Swappable: --set quantifier=kallisto | salmon (default salmon).

8 stage(s):

kallisto_index — quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0
kallisto_quant — quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0
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:2.4.1--hfa8f182_0
salmon_quant — quay.io/biocontainers/salmon:2.4.1--hfa8f182_0
deseq2_diff — quay.io/biocontainers/bioconductor-deseq2:1.50.2--r45ha27e39d_0
enrich_go — quay.io/biocontainers/gseapy:1.3.1--py311heb3b1e3_0

`scrna_seq`¶

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

Swappable: --set counter=kb | starsolo (default starsolo).

4 stage(s):

kb_ref — quay.io/biocontainers/kb-python:0.28.2--pyhdfd78af_2
kb_count — quay.io/biocontainers/kb-python:0.28.2--pyhdfd78af_2
starsolo — quay.io/biocontainers/star:2.7.11b--h43eeafb_0
scanpy_analyze — ghcr.io/hope9901/bioflow-scanpy:1.12.2

Recipes¶

Swappable stages (--set)¶

amr_vf_catalogue¶

ani_matrix¶

atac_seq¶

cafe_evolution¶

chip_seq¶

cog_enrichment¶

download_taxon¶

eukaryote_assembly¶

germline_variants¶

gwas¶

joint_genotyping¶

metagenome_assembly¶

metagenomics_profile¶

methylation_wgbs¶

pangenome¶

phylogeny¶

prokaryote_assembly¶

proteomics_dda¶

rnaseq_deg¶

scrna_seq¶

Swappable stages (`--set`)¶

`amr_vf_catalogue`¶

`ani_matrix`¶

`atac_seq`¶

`cafe_evolution`¶

`chip_seq`¶

`cog_enrichment`¶

`download_taxon`¶

`eukaryote_assembly`¶

`germline_variants`¶

`gwas`¶

`joint_genotyping`¶

`metagenome_assembly`¶

`metagenomics_profile`¶

`methylation_wgbs`¶

`pangenome`¶

`phylogeny`¶

`prokaryote_assembly`¶

`proteomics_dda`¶

`rnaseq_deg`¶

`scrna_seq`¶