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add csv syntax highlighting in template #2503

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Nov 8, 2023
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add csv syntax highlighting in template #2503

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fc1f219
add csv syntax highlighting in template
mashehu Nov 8, 2023
82a355d
update changelog
mashehu Nov 8, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -4,7 +4,8 @@

### Template

- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465)
- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465))
- Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))

### Linting

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4 changes: 2 additions & 2 deletions nf_core/pipeline-template/docs/usage.md
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Expand Up @@ -24,7 +24,7 @@ You will need to create a samplesheet with information about the samples you wou

The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
Expand All @@ -37,7 +37,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th

A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.

```console
```csv title="samplesheet.csv"
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
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