Merge pull request #45 from SusiJo/add_test_ymls

Add test yml files

.github/workflows/awsfulltest.yml

@@ -15,9 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.gitignore

@@ -7,4 +7,4 @@ testing/
 testing*
 *.pyc
 *.fasta
-*.fai
+*.fai

.nf-core.yml

@@ -1,3 +1,8 @@
 repository_type: pipeline
 lint:
+  files_exist:
+    - conf/igenomes.config
+  files_unchanged:
+    - .github/workflows/branch.yml
+    - lib/NfcoreSchema.groovy
   template_strings: False

CHANGELOG.md

@@ -6,8 +6,13 @@ Initial release of nf-core/bamtofastq, created with the [nf-core](https://nf-co.
 
 ### `Added`
 
+- [#45](https://github.com/nf-core/bamtofastq/pull/45) Add `test.yml` files with md5sums
+- [#44](https://github.com/nf-core/bamtofastq/pull/44) DSL2 conversion
+
 ### `Fixed`
 
+- [#45](https://github.com/nf-core/bamtofastq/pull/45) Minor bugfix with chromosome extraction
+
 ### `Dependencies`
 
 ### `Deprecated`

CITATIONS.md

@@ -12,11 +12,15 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
-- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
+- [SAMtools](https://doi.org/10.1093/gigascience/giab008)
+
+  > Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. D., Li, H., (2021) Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, giab008. doi: 10.1093/gigascience/giab008
 
   > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
 
@@ -36,5 +40,7 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

README.md

@@ -1,6 +1,6 @@
 # ![nf-core/bamtofastq](docs/images/nf-core-bamtofastq_logo_light.png#gh-light-mode-only) ![nf-core/bamtofastq](docs/images/nf-core-bamtofastq_logo_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bamtofastq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bamtofastq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.4022138-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.4022138)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -16,8 +16,6 @@
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
-<!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
-
 On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/bamtofastq/results).
 
 ## Pipeline summary
@@ -31,6 +29,10 @@ By default, the pipeline currently performs the following steps:
 5. QC of converted fastq reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)).
 6. Summarize QC and statistics before and after format conversion ([`MultiQC`](http://multiqc.info/)).
 
+<p align="center">
+    <img title="Bamtofastq Workflow" src="docs/images/nf-core-bamtofastq-subway.png" width=60%>
+</p>
+
 ## Quick Start
 
 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)

assets/methods_description_template.yml

@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/bamtofastq Methods Description"
 section_href: "https://github.com/nf-core/bamtofastq"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/bamtofastq v${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>
@@ -13,7 +11,16 @@ data: |
   <h4>References</h4>
   <ul>
     <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>
-    <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>
+    <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. <br><a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+    <li>Hanssen, F. (2022) nf-core/bamtofastq <a href="https://doi.org/10.5281/zenodo.4022138">https://doi.org/10.5281/zenodo.4022138</a></li>
+    <li>Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></li>
+    <li>Ewels, P. A., Magnusson, M., Lundin, S., Käller, S., MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, Volume 32, Issue 19, October 2016, Pages 3047–3048. <a href="https://doi.org/10.1093/bioinformatics/btw354">https://doi.org/10.1093/bioinformatics/btw354</a></li>
+    <li>Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. D., Li, H., (2021) Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, giab008. <a href="https://doi.org/10.1093/gigascience/giab008">https://doi.org/10.1093/gigascience/giab008</a></li>
+    <li>Anaconda Software Distribution. (2020). Anaconda Documentation. Anaconda Inc. Retrieved from <a href="https://anaconda.com">https://anaconda.com</a></li>
+    <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.  <a href="https://doi.org/10.1038/s41592-018-0046-7">https://doi.org/10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost F., Grüning B., Aflitos S. A., Röst H. L., Uszkoreit J., Barsnes H., Vaudel M., Moreno P., Gatto L., Weber J., Bai M., Jimenez R. C., Sachsenberg T., Pfeuffer J., Alvarez R. V., 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. <a href="https://doi.org/10.1093/bioinformatics/btx192">https://doi.org/10.1093/bioinformatics/btx192</a></li>
+    <li>Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. <a href="https://dl.acm.org/doi/10.5555/2600239.2600241">https://dl.acm.org/doi/10.5555/2600239.2600241</a></li>
+    <li>Kurtzer GM., Sochat V., Bauer MW. (2017). Singularity: Scientific containers for mobility of compute. PLoS One, 12(5):e0177459. <a href="https://doi.org/10.1371/journal.pone.0177459">https://doi.org/10.1371/journal.pone.0177459</a></li>
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>