oxo-call 0.11.0

Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
Documentation 
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# =============================================================================
# WGBS / Methylation sequencing workflow — oxo-call native format
#
# Usage:
#   1. Edit [wildcards] and [params] sections below
#   2. Run:  oxo-call workflow run methylseq.toml
#   3. Or preview first:  oxo-call workflow dry-run methylseq.toml
#   4. Export to Snakemake:  oxo-call workflow export methylseq.toml --to snakemake
#   5. Export to Nextflow:   oxo-call workflow export methylseq.toml --to nextflow
#
# Expected input layout:
#   data/{sample}_R1.fastq.gz
#   data/{sample}_R2.fastq.gz
#
# Required reference files:
#   bismark_index — directory containing bismark-prepared genome (bismark_genome_preparation)
# =============================================================================

[workflow]
name        = "methylseq"
description = "WGBS methylation: Trim Galore QC → MultiQC / Bismark alignment (parallel) → deduplication → methylation extraction → bismark2bedGraph"
version     = "1.0"

[wildcards]
sample = ["sample1", "sample2", "sample3"]

# ── Configurable parameters ───────────────────────────────────────────────────
# REQUIRED: update paths before running.
[params]
threads       = "8"
bismark_index = "/path/to/bismark_genome"   # REQUIRED: directory with bismark genome preparation output
genome_fasta  = "/path/to/genome.fa"        # REQUIRED: reference genome FASTA (for coverage calc)

# =============================================================================

[[step]]
name    = "trim_galore"
cmd     = """\
trim_galore \
  --paired \
  --cores {params.threads} \
  --fastqc \
  --illumina \
  --output_dir trimmed/ \
  data/{sample}_R1.fastq.gz \
  data/{sample}_R2.fastq.gz\
"""
inputs  = ["data/{sample}_R1.fastq.gz", "data/{sample}_R2.fastq.gz"]
outputs = ["trimmed/{sample}_R1_val_1.fq.gz", "trimmed/{sample}_R2_val_2.fq.gz",
           "trimmed/{sample}_R1_val_1_fastqc.zip"]

[[step]]
name       = "multiqc"
gather     = true
depends_on = ["trim_galore"]
cmd        = "multiqc trimmed/ -o results/multiqc/ --force"
inputs     = []
outputs    = ["results/multiqc/multiqc_report.html"]

[[step]]
name       = "bismark_align"
depends_on = ["trim_galore"]
cmd        = """\
bismark \
  --genome {params.bismark_index} \
  -1 trimmed/{sample}_R1_val_1.fq.gz \
  -2 trimmed/{sample}_R2_val_2.fq.gz \
  --output_dir aligned/ \
  --prefix {sample} \
  --parallel {params.threads} \
  --non_directional\
"""
inputs  = ["trimmed/{sample}_R1_val_1.fq.gz", "trimmed/{sample}_R2_val_2.fq.gz"]
outputs = ["aligned/{sample}_bismark_bt2_pe.bam",
           "aligned/{sample}_bismark_bt2_PE_report.txt"]

[[step]]
name       = "bismark_dedup"
depends_on = ["bismark_align"]
cmd        = """\
deduplicate_bismark \
  --paired \
  --output_dir deduped/ \
  aligned/{sample}_bismark_bt2_pe.bam\
"""
inputs  = ["aligned/{sample}_bismark_bt2_pe.bam"]
outputs = ["deduped/{sample}_bismark_bt2_pe.deduplicated.bam",
           "deduped/{sample}_bismark_bt2_pe.deduplication_report.txt"]

[[step]]
name       = "sort_index"
depends_on = ["bismark_dedup"]
cmd        = """\
samtools sort -@ {params.threads} \
  -o deduped/{sample}.sorted.bam \
  deduped/{sample}_bismark_bt2_pe.deduplicated.bam && \
samtools index deduped/{sample}.sorted.bam\
"""
inputs  = ["deduped/{sample}_bismark_bt2_pe.deduplicated.bam"]
outputs = ["deduped/{sample}.sorted.bam", "deduped/{sample}.sorted.bam.bai"]

[[step]]
name       = "methylation_extract"
depends_on = ["sort_index"]
cmd        = """\
bismark_methylation_extractor \
  --paired-end \
  --comprehensive \
  --CX_context \
  --cytosine_report \
  --genome_folder {params.bismark_index} \
  --output methyl/ \
  --parallel {params.threads} \
  deduped/{sample}.sorted.bam\
"""
inputs  = ["deduped/{sample}.sorted.bam"]
outputs = ["methyl/{sample}.sorted_CpG.bedGraph",
           "methyl/{sample}.sorted.bismark.cov.gz",
           "methyl/{sample}.sorted_splitting_report.txt"]

[[step]]
name       = "bismark2bedgraph"
depends_on = ["methylation_extract"]
cmd        = """\
bismark2bedGraph \
  --CX_context \
  --output {sample}.CpG.bedGraph \
  --dir methyl/ \
  methyl/CpG_OT_{sample}.sorted.txt \
  methyl/CpG_OB_{sample}.sorted.txt\
"""
inputs  = ["methyl/{sample}.sorted_CpG.bedGraph"]
outputs = ["methyl/{sample}.CpG.bedGraph.gz.bismark.zero.cov"]