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Start the documentation of output.md

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@ -13,6 +13,13 @@ The directories listed below will be created in the results directory after the
The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
- [FastQC](#fastqc) - Raw read QC - [FastQC](#fastqc) - Raw read QC
- [falco](#falco) - Alternative to FastQC for raw read QC
- [fastp](#fastp) - Adapter trimming for Illumina data
- [AdapterRemoval](#adapterremoval) - Adapter trimming for Illumina data
- [Porechop](#porechop) - Adapter removal for Oxford Nanopore data
- [BBDuk](#bbduk) - Quality trimming and filtering for Illumina data
- [PRINSEQ++](#prinseq++) - Quality trimming and filtering for Illunina data
- [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@ -37,6 +44,69 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. > **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
### fastp
fastp can automatically detect adapter sequences for Illumina data.
<details markdown="1">
<summary>Output files</summary>
- `fastp`
</details>
### AdapterRemoval
<details markdown="1">
<summary>Output files</summary>
- `adapterremoval`
</details>
### Porechop
<details markdown="1">
<summary>Output files</summary>
- `porechop`
- `<sample_id>.fastq.gz`
</details>
### BBDuk
<details markdown="1">
<summary>Output files</summary>
- `bbduk`
- `<sample_id>.bbduk.log`
- `<sample_id>.fastq.gz`
</details>
### PRINSEQ++
<details markdown="1">
<summary>Output files</summary>
- `prinseq++`
</details>
### Filtlong
<details markdown="1">
<summary>Output files</summary>
- `filtlong`
- `<sample_id>_filtered.fastq.g`
- `<sample_id>_filtered.log`
</details>
### MultiQC ### MultiQC
<details markdown="1"> <details markdown="1">