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Fix indent

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drpatelh 2020-08-06 16:18:16 +01:00
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@ -122,15 +122,17 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
bwa mem | samtools view -B -T ref.fasta
```
- Where applicable, the usage/generation of compressed files SHOULD be enforced as input/output e.g. `*.fastq.gz` and NOT `*.fastq`, `*.bam` and NOT `*.sam` etc.
- Where applicable, the usage and generation of compressed files SHOULD be enforced as input and output, respectively:
- `*.fastq.gz` and NOT `*.fastq`
- `*.bam` and NOT `*.sam`
- A module MUST NOT contain a `when` statement.
- Where applicable, each module command MUST emit a file `<SOFTWARE>.version.txt` containing a single line with the software's version in the format `<VERSION_NUMBER>` or `0.7.17`:
- Where applicable, each module command MUST emit a file `<SOFTWARE>.version.txt` containing a single line with the software's version in the format `<VERSION_NUMBER>` or `0.7.17` e.g.
```bash
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
```
If the software is unable to output a version number on the command-line then a variable called `VERSION` can be manually specified to create this file e.g. [homer/annotatepeaks module](https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf).
If the software is unable to output a version number on the command-line then a variable called `VERSION` can be manually specified to create this file e.g. [homer/annotatepeaks module](https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf).
#### Naming conventions