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Merge pull request #991 from bebatut/host-contamination-removal
Add 2 workflows (long and short-reads) for host and contamination removal from microbiome data
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‎workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/.dockstore.yml‎

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version: 1.2
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workflows:
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- name: main
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subclass: Galaxy
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publish: true
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primaryDescriptorPath: /host-or-contamination-removal-on-long-reads.ga
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testParameterFiles:
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- /host-or-contamination-removal-on-long-reads-tests.yml
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authors:
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- name: Paul Zierep
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orcid: 0000-0003-2982-388X
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- name: "B\xE9r\xE9nice Batut"
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orcid: 0000-0001-9852-1987

‎workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/CHANGELOG.md‎

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# Changelog
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## [0.1] 2025-12-03
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First release.

‎workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/README.md‎

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# Host or Contamination removal on long-reads
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The extraction of microbiome DNA or RNA is usually contaminated by host and human DNA or RNA (but also other contaminant). It is an important to get rid of all host/contamination sequences and to only retain microbiome sequences, both in order to speed up further steps and to avoid host/contamination sequences compromising the analysis.
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This workflow takes Nanopore fastq(.gz) files and executes the following steps:
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1. Mapping of the reads against a reference genome of the host or contaminant (e.g. human) using **Minimap 2**
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2. Filtering of the generated BAM using **BAMtools** and **Samtools** to keep only the reads that do not align
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3. Generation of mapping statistics using **QualiMap**
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4. Aggregation of the mapping statistics using **MultiQC**
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## Input Datasets
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- A list of datasets corresponding to reads in `fastqsanger` or `fastqsanger.gz` format.
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- Reference genome
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- Profile for mapping
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## Output Datasets
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- A list of datasets corresponding to unmapped reads in `fastqsanger` or `fastqsanger.gz`.
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- A list of reports of QualiMap for each sample that could be used as inputs for extra MultiQC
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- MultiQC report of the mapping statistics in HTML
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## When to use this workflow
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Use this workflow for **long-read sequencing data** (e.g., Nanopore, PacBio). For short-read Illumina data, see the [Host or Contamination removal on short-reads](../host-contamination-removal-short-reads/) workflow.

‎workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml‎

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- doc: Test outline for host-or-contamination-removal-on-long-reads
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job:
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Long-reads:
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class: Collection
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collection_type: list
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elements:
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- class: File
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identifier: Spike3bBarcode10
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location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode10.fastq.gz
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filetype: fastqsanger.gz
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- class: File
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identifier: Spike3bBarcode12
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location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode12.fastq.gz
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filetype: fastqsanger.gz
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Host/Contaminant Reference Genome (long-reads): apiMel3
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Profile of preset options for the mapping (long-read): map-pb
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outputs:
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QualiMap Statistics:
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element_tests:
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Spike3bBarcode10:
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elements:
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genome_results:
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asserts:
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has_text:
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text: "Spike3bBarcode10"
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has_text:
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text: "586,300,787 bp"
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coverage_across_reference:
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asserts:
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has_text:
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text: "#Position (bp)"
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has_n_lines:
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value: 416
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coverage_histogram:
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asserts:
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has_text:
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text: "Number of genomic locations"
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has_n_lines:
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value: 10
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genome_fraction_coverage:
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asserts:
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has_text:
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text: "#Coverage (X)"
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has_n_lines:
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value: 51
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duplication_rate_histogram:
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asserts:
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has_text:
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text: "#Duplication rate"
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has_text:
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text: "17.0"
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homopolymer_indels:
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asserts:
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has_text:
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text: "#Type of indel"
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has_text:
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text: "polyN"
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insert_size_across_reference:
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asserts:
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has_size:
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value: 0
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insert_size_histogram:
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asserts:
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has_size:
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value: 0
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mapped_reads_clipping_profile:
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asserts:
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has_text:
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text: "#Read position (bp)"
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has_text:
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text: "38.123"
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mapped_reads_gc-content_distribution:
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asserts:
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has_text:
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text: "#GC Content (%)"
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has_n_lines:
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value: 100
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mapped_reads_nucleotide_content:
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asserts:
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has_text:
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text: "6.25"
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mapping_quality_across_reference:
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asserts:
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has_text:
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text: "#Position (bp)"
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has_n_lines:
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value: 416
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mapping_quality_histogram:
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asserts:
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has_text:
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text: "#Mapping quality"
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has_n_lines:
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value: 13
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Spike3bBarcode12:
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elements:
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genome_results:
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asserts:
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has_text:
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text: "Spike3bBarcode12"
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has_text:
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text: "586,300,787 bp"
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coverage_across_reference:
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asserts:
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has_text:
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text: "#Position (bp)"
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has_n_lines:
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value: 416
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coverage_histogram:
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asserts:
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has_text:
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text: "Number of genomic locations"
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has_n_lines:
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value: 6
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genome_fraction_coverage:
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asserts:
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has_text:
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text: "#Coverage (X)"
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has_n_lines:
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value: 51
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duplication_rate_histogram:
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asserts:
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has_text:
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text: "#Duplication rate"
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has_text:
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text: "8.0"
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homopolymer_indels:
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asserts:
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has_text:
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text: "#Type of indel"
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has_text:
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text: "polyN"
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insert_size_across_reference:
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asserts:
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has_size:
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value: 0
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insert_size_histogram:
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asserts:
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has_size:
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value: 0
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mapped_reads_clipping_profile:
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asserts:
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has_text:
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text: "#Read position (bp)"
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has_text:
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text: "0.03930972"
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mapped_reads_gc-content_distribution:
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asserts:
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has_text:
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text: "#GC Content (%)"
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has_n_lines:
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value: 100
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mapped_reads_nucleotide_content:
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asserts:
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has_text:
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text: "16.0"
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mapping_quality_across_reference:
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asserts:
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has_text:
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text: "#Position (bp)"
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has_n_lines:
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value: 416
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mapping_quality_histogram:
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asserts:
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has_text:
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text: "#Mapping quality"
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has_n_lines:
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value: 4
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MultiQC HTML Report:
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asserts:
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has_text:
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text: "Spike3bBarcode10"
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has_text:
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text: "Spike3bBarcode12"
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Reads without Host or Contamination:
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element_tests:
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Spike3bBarcode10:
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asserts:
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has_text:
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text: "@0a0c4d2c-291f-46a4-87d5-625efbfed6a0"
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Spike3bBarcode12:
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asserts:
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has_text:
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text: "@0a0c4e88-893a-4284-9119-ab4274e05445"

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