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fix console indentation
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Daniel-VM committed Oct 23, 2023
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Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions README.md
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Expand Up @@ -64,21 +64,21 @@ Each row represents a fastq file (single-end) or a pair of fastq files (paired e

Default: Short read assembly with Unicycler, `--kraken2db` can be any [compressed database (`.tar.gz`/`.tgz`)](https://benlangmead.github.io/aws-indexes/k2):

```console
nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
```
```console
nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
```

Long read assembly with Miniasm:
Long read assembly with Miniasm:

```console
nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --assembly_type 'long' --assembler 'miniasm' --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
```
```console
nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --assembly_type 'long' --assembler 'miniasm' --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
```

```bash
nextflow run nf-core/bacass \
-profile <docker/singularity/.../institute> \
--input samplesheet.tsv \
--outdir <OUTDIR>
-profile <docker/singularity/.../institute> \
--input samplesheet.tsv \
--outdir <OUTDIR>
```

:::warning
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