Merge branch 'dev' into nf-core-template-merge-2.12.1

.github/workflows/build-docker-image.yml

@@ -0,0 +1,27 @@
+name: Publish Docker image for PrepareAA
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Quay.io
+        uses: docker/login-action@v2
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAYIO_CIRCDNA_USERNAME }}
+          password: ${{ secrets.QUAYIO_CIRCDNA_PASSWORD }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          file: modules/local/ampliconsuite/Dockerfile
+          push: true
+          tags: "quay.io/nf-core/prepareaa:1.0.5"

.github/workflows/ci.yml

@@ -36,8 +36,27 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+  test_AA:
+    name: Run pipeline with test data and ensure AmpliconSuite Installation
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/circdna') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_AA,docker --outdir ./results

.github/workflows/download_pipeline.yml

@@ -64,4 +64,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results 
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

.gitignore

@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+null
+.vscode

.gitpod.yml

@@ -7,7 +7,6 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
-
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

.nf-core.yml

@@ -1 +1,12 @@
 repository_type: pipeline
+
+lint:
+  files_exist:
+    - assets/multiqc_config.yml
+  files_unchanged:
+    - assets/email_template.html
+
+update:
+  nf-core:
+    samtools/sort: "1ad73f1b2abdea9398680d6d20014838135c9a35"
+    samtools/index: "1ad73f1b2abdea9398680d6d20014838135c9a35"

CHANGELOG.md

@@ -3,14 +3,113 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.1 - [date]
+## v1.1 - [2024-01-30]
 
-Initial release of nf-core/circdna, created with the [nf-core](https://nf-co.re/) template.
+### Credits
+
+Special thanks to the following for their input and contributions to the release:
+
+- [Jens Luebeck](https://github.com/jluebeck)
+- [Simon Pearce](https://github.com/SPPearce)
+- [Maxime U Garcia](https://github.com/maxulysse)
+
+### Enhancements & fixes
+
+- Nf-core template update to 2.11.1
+  - update of nf-core modules versions
+- Removed AmpliconArchitect and AmpliconClassifier modules with their respective scripts in /bin
+  - AmpliconArchitect and AmpliconClassifier is now run inside the AmpliconSuite-Pipeline. Additional scripts are not necessary.
+  - Removed respective configs and workflow code
+- Added AmpliconSuite-Pipeline
+  - A wrapper for calling copy numbers, preparing amplified intervals, running AmpliconArchitect, and calling amplicon classes using AmpliconClassifier
+  - Added docker container named [PrepareAA](https://quay.iorepository/nf-core/prepareaa?tab=tags) to run AmpliconSuite-Pipeline with singualarity or docker
+  - Added module configs and description
+- Changed `assets/multiqc_config.yml`to fit new pipeline version
+- Included directory checks for `mosek_license_dir` and `aa_data_repo` .
+  - Removed both directory parameters in the test profile as it is only checked when running `ampliconarchitect`
+- Updated `nextflow_schema.json` to give better details about how to use `--circle_identifier`
+- made `--circle_identifier` an essential parameter
+
+## v1.0.4 - [2023-06-26]
+
+### `Added`
+
+### `Fixed`
+
+- Bug that the pipeline only runs with one sample when Picard Markduplicates is used
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.0.3 - [2023-05-26]
+
+### `Added`
+
+- Licence, contact, source information for AmpliconArchitect and PrepareAA python scripts
+- documentation about absolute path needed of AmpliconArchitect data repository
+- ampliconclassifier stub run tests
+- new version of circdna metromap with updated colors
+- note that ATAC-seq should be used in caution with the pipeline.
+- build docker container for prepareaa -> Needs to be built first and will be included in the next release
+- nf-core template update 2.8
+
+### `Fixed`
+
+- Circle_finder bug with bash sort command wanting to write into /tmp/ directory and not into work directory
+- Usage.md updated to new paths and addition of nf-core modules
+
+### `Dependencies`
+
+### `Deprecated`
+
+- Local python scripts not included in the pipeline
+- Local versions of nf-core modules
+
+## v1.0.2 - [2023-03-07]
+
+### `Added`
+
+- ampliconclassifier/makeinput module added -> Generates the input file used for ampliconclassifier functions
+- ampliconclassifier/makeresultstable added -> Generates results table from AmpliconArchitect and AmpliconClassifier
+- CNN Reference File For AmpliconArchitect
+- mm10 option for AmpliconArchitect
+- stub runs for AmpliconArchitect processes
+- New module versions
+- nf-core template 2.7.2
+
+### `Fixed`
+
+- Fixed ZeroDivisionError by Circle-Map
+- Fixed keep_duplicates and skip_markduplicates parameter bug
+
+### `Dependencies`
+
+### `Deprecated`
+
+- AmpliconArchitect Summary Process was deprecated
+
+## v1.0.1 - [2022-06-22]
 
 ### `Added`
 
+- Documentation Updates
+
 ### `Fixed`
 
+- Fixed Bug with pipeline version in nextflow.config
+- Fixed Circle-Map Realign bug in which only one sample is processed
+
 ### `Dependencies`
 
 ### `Deprecated`
+
+- Samtools FAIDX
+
+## v1.0.0 - [2022-06-01]
+
+Initial release of nf-core/circdna, created with the [nf-core](https://nf-co.re/) template.
+
+nf-core/circdna is a bioinformatics analysis pipeline for the identification of circular DNAs in eukaryotic cells. The pipeline is able to process WGS, ATAC-seq data or Circle-Seq data to give insights into the circular DNA landscape in your samples.
+
+In total, the user can choose between 5 different branches inside the pipeline, depending on the biological question and the input data set. In these branches, specific software is used that is built for either the identification of amplified circular DNAs, the detection of putative circular DNA junctions, or the de novo assembly and mapping of circular DNAs.

CITATIONS.md

@@ -18,6 +18,51 @@
 
   > 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](http://www.htslib.org/)
+
+  > 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. PMID: 19505943; PMCID: PMC2723002.
+
+- [Trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+
+- [BWA](https://github.com/lh3/bwa)
+
+  > Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
+
+- [Picard](https://broadinstitute.github.io/picard/)
+
+- [Circle-Map](https://github.com/iprada/Circle-Map)
+
+  > Prada-Luengo I, Krogh A, Maretty L, Regenberg B. Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. BMC Bioinformatics. 2019 Dec 12;20(1):663. doi: 10.1186/s12859-019-3160-3. PMID: 31830908; PMCID: PMC6909605.
+
+- [Unicycler](https://github.com/rrwick/Unicycler)
+
+  > Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. PMID: 28594827; PMCID: PMC5481147.
+
+- [CNVKit](https://github.com/etal/cnvkit)
+
+  > Talevich E, Shain AH, Botton T, Bastian BC. Cnvkit: genome-wide copy number detection and visualization from targeted dna sequencing. PLoS Comput Biol. 2016;12(4):e1004873. doi: 10.1371/journal.pcbi.1004873. PMID: 27100738; PMCID: PMC4839673.
+
+- [AmpliconSuite-Pipeline](https://github.com/AmpliconSuite/AmpliconSuite-pipeline)
+
+- [AmpliconArchitect](https://github.com/virajbdeshpande/AmpliconArchitect)
+
+  > Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun. 2019 Jan 23;10(1):392. doi: 10.1038/s41467-018-08200-y. PMID: 30674876; PMCID: PMC6344493.
+
+- [AmpliconClassifier](https://github.com/jluebeck/AmpliconClassifier)
+
+  > Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Nature. 2023 Apr;616(7958):798-805. doi: 10.1038/s41586-023-05937-5. Epub 2023 Apr 12. PMID: 37046089; PMCID: PMC10132967.
+
+- [Samblaster](https://github.com/GregoryFaust/samblaster)
+
+  > Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014 Sep 1;30(17):2503-5. doi: 10.1093/bioinformatics/btu314. Epub 2014 May 7. PMID: 24812344; PMCID: PMC4147885.
+
+- [Circle_finder](https://github.com/pk7zuva/Circle_finder)
+
+  > Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Mol Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. Epub 2017 May 26. PMID: 28550083; PMCID: PMC5581709.
+
+- [Circexplorer2](https://circexplorer2.readthedocs.io/en/latest/)
+  > Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87. doi: 10.1101/gr.202895.115. Epub 2016 Jun 30. PMID: 27365365; PMCID: PMC5052039.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)