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Add info on Nanopore reads to fastq_1 column

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ljmesi 2022-03-18 11:00:36 +01:00
parent 7f7ddc9f14
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docs/usage.md
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@ -44,11 +44,11 @@ TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
``` ```
| Column | Description | | Column | Description |
|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | | `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_1` | Full path to FastQ file for Illumina short reads 1 or Nanopore reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". |
An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.