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Add classifiers
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@ -20,6 +20,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
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- [BBDuk](#bbduk) - Quality trimming and filtering for Illumina data
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- [PRINSEQ++](#prinseq++) - Quality trimming and filtering for Illunina data
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- [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
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- [Bowtie2](#bowtie2) - Host removal for Illumina reads
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- [minimap2](#minimap2) - Host removal for Nanopore reads
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- [samtoolsstats](#samtoolsstats) - Statistics from host removal
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- [cat] - **WIP**
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- [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
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- [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
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- [Bracken](#bracken) -
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- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
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- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
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@ -105,6 +112,74 @@ fastp can automatically detect adapter sequences for Illumina data.
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</details>
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### Bowtie2
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<details markdown="1">
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<summary>Output files</summary>
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- `bowtie2`
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- `<sample_id>.bam`
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- `<sample_id>.bowtie2.log`
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- `<sample_id>.unmapped.fastq.gz`
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</details>
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### minimap2
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<details markdown="1">
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<summary>Output files</summary>
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- `minimap2`
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- `<sample_id>.bam`
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</details>
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### Samtools stats
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<details markdown="1">
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<summary>Output files</summary>
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- `samtoolsstats`
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- `<sample_id>.stats`
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</details>
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### cat
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<details markdown="1">
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<summary>Output files</summary>
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- `cat`
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</details>
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### Kraken2
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<details markdown="1">
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<summary>Output files</summary>
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- `kraken2`
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- `<sample_id>.classified.fastq.gz`
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- `<sample_id>.unclassified.fastq.gz`
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- `<sample_id>.report.txt`
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- `<sample_id>.classifiedreads.txt`
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</details>
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### KrakenUniq
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<details markdown="1">
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<summary>Output files</summary>
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- `krakenuniq`
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- `<sample_id>.classified.fastq.gz`
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- `<sample_id>.krakenuniq.classified.txt`
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- `<sample_id>.krakenuniq.report.txt`
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- `<sample_id>.unclassified.fastq.gz`
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## interleaved?
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</details>
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### MultiQC
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