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[automated] Fix code linting
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nf-core-bot committed Mar 19, 2024
1 parent 0eff5e6 commit 30548ad
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -31,12 +31,12 @@ SINGLE_END_SHORT_LONG,AEG588A4_S1_L002_R1_001.fastq.gz,,AEG588A4_001.fastq.gz
PAIRED_END_PLUS_LONG,AEG588A5_S1_L002_R1_001.fastq.gz,AEG588A5_S1_L002_R2_001.fastq.gz,AEG588A5_001.fastq.gz
```

| 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 (`_`). |
| `short_reads_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". Optional, if `long_reads_fastq_1` is also provided. |
| 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 (`_`). |
| `short_reads_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". Optional, if `long_reads_fastq_1` is also provided. |
| `short_reads_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". Optional. Only used for paired-end files. |
| `long_reads_fastq_1` | Full path to FastQ file for long reads. File has to be gzipped and have the extension ".fastq.gz" or "fq.gz". Optional. Use only for long reads. |
| `long_reads_fastq_1` | Full path to FastQ file for long reads. File has to be gzipped and have the extension ".fastq.gz" or "fq.gz". Optional. Use only for long reads. |

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

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