You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
Copy file name to clipboardExpand all lines: README.md
+16-16Lines changed: 16 additions & 16 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -2,7 +2,7 @@
2
2
3
3
[](https://nf-co.re/smrnaseq/results)[](https://doi.org/10.5281/zenodo.3456879)
<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
79
-
80
80
```bash
81
81
nextflow run nf-core/smrnaseq \
82
82
-profile <docker/singularity/.../institute> \
83
-
--input samplesheet.csv \
84
-
--genome 'GRCh37' \
85
-
--mirtrace_species 'hsa' \
86
-
--protocol 'illumina' \
87
-
--outdir <OUTDIR>
83
+
--input samplesheet.csv \
84
+
--genome 'GRCh37' \
85
+
--mirtrace_species 'hsa' \
86
+
--protocol 'illumina' \
87
+
--outdir <OUTDIR>
88
88
```
89
89
90
90
> **Warning:**
91
91
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
92
92
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
93
93
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
94
94
95
-
For more details, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters).
95
+
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/smrnaseq/usage) and the [parameter documentation](https://nf-co.re/smrnaseq/parameters).
96
96
97
97
## Pipeline output
98
98
99
-
To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page.
99
+
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/smrnaseq/results) tab on the nf-core website pipeline page.
100
100
For more details about the output files and reports, please refer to the
<p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
8
+
<p>Data was processed using nf-core/smrnaseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
9
9
<p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
10
10
<pre><code>${workflow.commandLine}</code></pre>
11
+
<p>${tool_citations}</p>
11
12
<h4>References</h4>
12
13
<ul>
13
-
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
14
-
<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
14
+
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
15
+
<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
16
+
<li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
17
+
<li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
0 commit comments