soapnuke

TAFFISH app for SOAPnuke, BGI's integrated quality control and preprocessing tool for high-throughput sequencing data.

This package builds upstream SOAPnuke 2.1.9 from source and exposes the upstream SOAPnuke executable through the versioned taf-soapnuke command. The TAFFISH package name is lowercase soapnuke; the upstream project and primary binary keep the original SOAPnuke capitalization.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install soapnuke

Install the exact release:

taf install soapnuke 2.1.9-r1

For local testing before the app is published to the public index:

taf install --from .

Usage

Show TAFFISH app help:

taf-soapnuke --help

Show the TAFFISH package version:

taf-soapnuke --version

Show the upstream SOAPnuke version:

taf-soapnuke SOAPnuke -v
taf-soapnuke soapnuke -v
taf-soapnuke -- -v

Show upstream module help:

taf-soapnuke SOAPnuke filter -h
taf-soapnuke SOAPnuke filterHts -h
taf-soapnuke SOAPnuke filterStLFR -h
taf-soapnuke SOAPnuke filtersRNA -h
taf-soapnuke SOAPnuke filterMeta -h

Run paired-end FASTQ filtering:

taf-soapnuke SOAPnuke filter \
  -1 reads_1.fq.gz \
  -2 reads_2.fq.gz \
  -C clean_1.fq.gz \
  -D clean_2.fq.gz \
  -o soapnuke_out \
  -T 8 \
  -l 5 \
  -q 0.5 \
  -n 0.05 \
  -4 30

Run single-end FASTQ filtering:

taf-soapnuke SOAPnuke filter \
  -1 reads.fq.gz \
  -C clean.fq.gz \
  -o soapnuke_out \
  -T 4 \
  -l 5 \
  -q 0.5 \
  -n 0.05 \
  -4 30

Run BAM/CRAM preprocessing through the htslib-enabled module:

taf-soapnuke SOAPnuke filterHts \
  -1 input.bam \
  -2 clean.bam \
  -o soapnuke_hts_out \
  -T 4 \
  -l 5 \
  -q 0.5 \
  -n 0.05 \
  -4 30

For CRAM input or CRAM output, pass the reference with -E as described by upstream help:

taf-soapnuke SOAPnuke filterHts \
  -E reference.fa \
  -1 input.cram \
  -2 clean.cram \
  -o soapnuke_hts_out

Run the upstream plotting scripts after SOAPnuke writes statistics files:

taf-soapnuke Rscript /opt/soapnuke/Rscripts/Q20Q30.R \
  soapnuke_out/Distribution_of_Q20_Q30_bases_by_read_position_1.txt \
  soapnuke_out/Distribution_of_Q20_Q30_bases_by_read_position_2.txt \
  q20_q30.png

TAFFISH Command Mode

This is a normal TAFFISH tool app with command_mode = true.

SOAPnuke itself uses module names such as filter, filterHts, filterStLFR, filtersRNA, and filterMeta. Prefer the explicit executable form:

taf-soapnuke SOAPnuke filter ...
taf-soapnuke SOAPnuke filterHts ...

Do not rely on:

taf-soapnuke filter ...

In command mode, a non-option first argument can be interpreted as a container executable name rather than as a SOAPnuke module. The explicit taf-soapnuke SOAPnuke ... form is unambiguous.

For option-leading arguments to the default upstream command, this also works:

taf-soapnuke -- -v
taf-soapnuke -- filter -h

The container also provides a lowercase soapnuke symlink to the same upstream binary. It is a convenience alias, not a separate implementation.

Package

name: soapnuke
command: taf-soapnuke
version: 2.1.9-r1
kind: tool
image: ghcr.io/taffish/soapnuke:2.1.9-r1
upstream: BGI-flexlab/SOAPnuke
upstream tag: SOAPnuke2.1.9

Container

The container image is built from docker/Dockerfile. It starts from debian:12-slim, downloads the official upstream SOAPnuke2.1.9 source archive from GitHub, verifies the SHA256 checksum, and builds the binary with USEHTS=true.

The image includes these user-facing commands:

SOAPnuke
soapnuke
samtools
Rscript

SOAPnuke is the upstream executable. soapnuke is a lowercase symlink for typing convenience. samtools and the htslib runtime are included for the filterHts BAM/CRAM module and for small local BAM/CRAM checks. Rscript is included so the upstream plotting scripts under /opt/soapnuke/Rscripts can be used directly.

The runtime also contains the upstream README, ChangeLog, and GPLv3 license text under /opt/soapnuke/share.

This app intentionally does not bundle reference genomes, adapter databases, contaminant databases, sequencing platform presets beyond upstream defaults, or downstream workflow orchestration. SOAPnuke's own modules and options are available as-is through the upstream command.

The image is built and validated for:

linux/amd64
linux/arm64

Functional Surface

Packaged upstream modules:

filter       normal FASTQ preprocessing
filterHts    BAM/CRAM preprocessing, built with htslib support
filterStLFR  stLFR FASTQ preprocessing
filtersRNA   small RNA FASTQ preprocessing
filterMeta   metagenomic FASTQ preprocessing

The upstream -v option prints the runtime version but exits non-zero. Smoke tests and examples capture the version text through grep; this is upstream behavior, not a TAFFISH wrapper change.

FASTQ inputs may be plain text or gzip-compressed. Paired-end inputs must use matching compression formats, and paired clean outputs must both be .gz or both be plain text, matching upstream validation.

Smoke Coverage

The smoke tests are independent and run without network access. They check:

• command presence for SOAPnuke, lowercase soapnuke, samtools, Rscript, gawk, gzip, ldd, and sh
• upstream runtime version 2.1.9
• help banners for filter, filterHts, filterStLFR, filtersRNA, and filterMeta
• dynamic linkage to htslib and zlib
• a tiny paired-end filter run that writes clean FASTQ plus statistics
• tiny filtersRNA and filterMeta FASTQ runs, including gzip input/output
• a tiny filterHts BAM run generated with bundled samtools
• availability of all three upstream R plotting scripts

These tests verify packaging, command availability, and small real execution paths. They are not a substitute for biological validation on production read sets, platform-specific adapter schemes, or full downstream QC review.

Upstream

• Upstream repository: https://github.com/BGI-flexlab/SOAPnuke
• Release: https://github.com/BGI-flexlab/SOAPnuke/releases/tag/SOAPnuke2.1.9
• Upstream license: GPL-3.0-only
• Citation: Chen et al. 2018, Gigascience
• DOI: 10.1093/gigascience/gix120
• PMID: 29220494

Maintainer Notes

Useful checks before publishing:

taf check
docker build -t ghcr.io/taffish/soapnuke:2.1.9-r1 -f docker/Dockerfile .
taf build
TAFFISH_CONTAINER_BACKEND=docker target/taf-soapnuke-v2.1.9-r1 -- -v
TAFFISH_CONTAINER_BACKEND=docker target/taf-soapnuke-v2.1.9-r1 SOAPnuke filter -h
taf publish --dry-run