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SAMtools

Read, write, and manipulate SAM, BAM, and CRAM alignment files

SAMtools provides utilities for sorting, indexing, filtering, and inspecting sequence alignments in the SAM/BAM/CRAM formats. In this workflow it runs a common step non-interactively: it sorts the input alignment, indexes it, and writes alignment statistics.

Key features:

  • Convert between SAM, BAM, and CRAM
  • Sort and index alignments for fast random access
  • Summarize alignments with flagstat and stats

Configuration

name: samtools
tags:
    - genomics
steps:
    - name: job
      platform: docker
      mode: parallel
      image: ghcr.io/dxflow-ai/samtools:latest
      volumes:
          - name: input
            host: ./input
            container: /data/input
            mode: ro
          - name: output
            host: ./output
            container: /data/output
      env:
          - INPUT=/data/input/sample.sam
          - THREADS=4
      resources:
          cpu: "4"
          memory: 4G

[volume]
job.input = ./input
job.output = ./output

[env]
job.INPUT = /data/input/sample.sam
job.THREADS = 4

[resource]
job.cpu = 4
job.memory = 4G

{
    "arch": ["amd64"],
    "image": "ghcr.io/dxflow-ai/samtools:latest",
    "version": "1.19",
    "minimum": {
        "cpu": 2,
        "memory": "2G",
        "storage": "10G"
    }
}

Usage

1. Prepare data

Upload an alignment file (SAM, BAM, or CRAM):

# Create input/output directories
mkdir -p input output

# Upload your alignment
dxflow artifact upload /local/sample.bam input/

2. Deploy

dxflow workflow create --identity samtools samtools.yml

3. Start (with optional tuning)

The step reads INPUT (the alignment to process) and THREADS (sort/compression threads). Override them per run:

# Start with defaults
dxflow workflow start samtools

# Or point at a BAM with more threads
dxflow workflow start samtools \
    --override env.job.INPUT=/data/input/sample.bam \
    --override env.job.THREADS=8

4. Retrieve results

dxflow artifact download output/ /local/samtools-results/

Output files

  • sorted.bam - the input coordinate-sorted
  • sorted.bam.bai - the BAM index
  • flagstat.txt - alignment counts (total, mapped, properly paired, duplicates)

Notes

  • INPUT accepts SAM, BAM, or CRAM — samtools detects the format automatically.
  • For custom pipelines (view, merge, mpileup, depth, …), run the container interactively or supply your own script; the default step covers the common sort → index → summarize path.

References

FastQC

Quality control tool for high throughput sequencing data

Pangolin

SARS-CoV-2 lineage assignment using the Pango nomenclature