Release 2.3 Updates: Fixes for contamination, UMI Handling, Template 2.11.1

.devcontainer/devcontainer.json

@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }

.github/CONTRIBUTING.md

@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
+receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/smrn
 - [ ] If necessary, also make a PR on the nf-core/smrnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -29,9 +29,10 @@ jobs:
         profile:
           - "test"
           - "test_no_genome"
+          - "test_umi"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - 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

CHANGELOG.md

@@ -3,9 +3,38 @@
 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).
 
-## [dev](https://github.com/nf-core/smrnaseq/branch/dev)
+## v2.3dev - [date]
 
-- _nothing yet done_
+- [[#299]](https://github.com/nf-core/smrnaseq/issues/299) - Bugfix for missing inputs in BAM stats (`genome_quant.r`)
+- [[#164]](https://github.com/nf-core/smrnaseq/pull/164) - UMI Handling Feature implemented in the pipeline
+- [[#302]](https://github.com/nf-core/smrnaseq/pull/302) - Merged in nf-core template v2.11.1
+- [[#294]](https://github.com/nf-core/smrnaseq/pull/294) - Fixed contamination screening issues
+
+### Parameters
+
+| Old parameter | New parameter               |
+| ------------- | --------------------------- |
+|               | `--with_umi`                |
+|               | `--umitools_extract_method` |
+|               | `--umitools_method`         |
+|               | `--skip_umi_extract`        |
+|               | `--umitools_bc_pattern`     |
+|               | `--umi_discard_read`        |
+|               | `--save_umi_intermeds`      |
+
+### Software dependencies
+
+| Dependency   | Old version | New version |
+| ------------ | ----------- | ----------- |
+| `multiqc`    | 1.15        | 1.19        |
+| `edgeR`      | 3.36.0      | 4.0.2       |
+| `limma`      | 3.50.0      | 3.58.1      |
+| `bioconvert` | 0.4.3       | 1.1.1       |
+| `mirdeep`    | 2.0.1       | 2.0.1.3     |
+| `seqkit`     | 2.3.1       | 2.6.1       |
+| `fastqc`     | 0.11.4      | 0.12.1      |
+| `samtools`   | 1.17        | 1.18        |
+| `umitools`   | <none>      | 1.1.4       |
 
 ## [v2.2.4](https://github.com/nf-core/smrnaseq/releases/tag/2.2.4) - 2023-11-03
 
@@ -64,23 +93,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#188](https://github.com/nf-core/smrnaseq/pull/188)] - Dropped TrimGalore in favor of fastp QC and adapter trimming, improved handling of adapters and trimming parameters
 - [[#194](https://github.com/nf-core/smrnaseq/issues/194)] - Added default adapters file for FastP improved miRNA adapter trimming
 
-### Parameters
-
-| Old parameter | New parameter            |
-| ------------- | ------------------------ |
-|               | `--mirgenedb`            |
-|               | `--mirgenedb_species`    |
-|               | `--mirgenedb_gff`        |
-|               | `--mirgenedb_mature`     |
-|               | `--mirgenedb_hairpin`    |
-|               | `--contamination_filter` |
-|               | `--rrna`                 |
-|               | `--trna`                 |
-|               | `--cdna`                 |
-|               | `--ncrna`                |
-|               | `--pirna`                |
-|               | `--other_contamination`  |
-
 ## [v2.0.0](https://github.com/nf-core/smrnaseq/releases/tag/2.0.0) - 2022-05-31 Aqua Zinc Chihuahua
 
 ### Major enhancements
@@ -98,20 +110,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Other enhancements & fixes
 
 - [#134](https://github.com/nf-core/smrnaseq/issues/134) - Fixed colSum of zero issues for edgeR_miRBase.R script
+- [#49](https://github.com/nf-core/smrnaseq/issues/49) - Integrated the existing umitools modules into the pipeline and extend the deduplication step.
 - [#55](https://github.com/lpantano/seqcluster/pull/55) - update seqcluster to fix UMI-detecting bug
 
-### Parameters
-
-| Old parameter        | New parameter    |
-| -------------------- | ---------------- |
-| `--conda`            | `--enable_conda` |
-| `--clusterOptions`   |                  |
-| `--publish_dir_mode` |                  |
-
-> **NB:** Parameter has been **updated** if both old and new parameter information is present.
-> **NB:** Parameter has been **added** if just the new parameter information is present.
-> **NB:** Parameter has been **removed** if parameter information isn't present.
-
 ### Software dependencies
 
 Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

README.md

@@ -27,37 +27,45 @@ You can find numerous talks on the nf-core events page from various topics inclu
 
 ## Pipeline summary
 
-1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
-   1. Insert Size calculation
-   2. Collapse reads ([`seqcluster`](https://seqcluster.readthedocs.io/mirna_annotation.html#processing-of-reads))
-3. Contamination filtering ([`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
-4. Alignment against miRBase mature miRNA ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
-5. Alignment against miRBase hairpin
-   1. Unaligned reads from step 3 ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
-   2. Collapsed reads from step 2.2 ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
-6. Post-alignment processing of miRBase hairpin
-   1. Basic statistics from step 3 and step 4.1 ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
-   2. Analysis on miRBase, or MirGeneDB hairpin counts ([`edgeR`](https://bioconductor.org/packages/release/bioc/html/edgeR.html))
-      - TMM normalization and a table of top expression hairpin
-      - MDS plot clustering samples
-      - Heatmap of sample similarities
-   3. miRNA and isomiR annotation from step 4.1 ([`mirtop`](https://github.com/miRTop/mirtop))
-7. Alignment against host reference genome ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
-   1. Post-alignment processing of alignment against host reference genome ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
-8. Novel miRNAs and known miRNAs discovery ([`MiRDeep2`](https://www.mdc-berlin.de/content/mirdeep2-documentation))
+1. Quality check and triming
+   1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+   2. Adapter trimming ([`fastp`](https://github.com/OpenGene/fastp))
+   3. UMI barcode extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
+   4. Trim read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. miRNA QC ([`miRTrace`](https://github.com/friedlanderlab/mirtrace))
+3. Contamination filtering ([`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) (Optional)
+   1. rRNA filtration
+   2. tRNA filtration
+   3. cDNA filtration
+   4. ncRNA filtration
+   5. piRNA filtration
+   6. Others filtration
+4. UMI barcode deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
+5. miRNA quantification
+   - EdgeR
+     1. Reads alignment against miRBase mature miRNA ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
+     2. Post-alignment processing of alignment against Mature miRNA ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
+     3. Unmapped reads (from reads vs mature miRNA) alignment against miRBase hairpin
+     4. Post-alignment processing of alignment against Hairpin ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
+     5. Analysis on miRBase, or MirGeneDB hairpin counts ([`edgeR`](https://bioconductor.org/packages/release/bioc/html/edgeR.html))
+        - TMM normalization and a table of top expression hairpin
+        - MDS plot clustering samples
+        - Heatmap of sample similarities
+   - Mirtop quantification
+     1. Read collapsing ([`seqcluster`](https://github.com/lpantano/seqcluster))
+     2. miRNA and isomiR annotation ([`mirtop`](https://github.com/miRTop/mirtop))
+6. Genome Quantification (Optional)
+   1. Reads alignment against host reference genome ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
+   2. Post-alignment processing of alignment against host reference genome ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
+7. Novel miRNAs and known miRNAs discovery ([`MiRDeep2`](https://www.mdc-berlin.de/content/mirdeep2-documentation)) (Optional)
    1. Mapping against reference genome with the mapper module
    2. Known and novel miRNA discovery with the mirdeep2 module
-9. miRNA quality control ([`mirtrace`](https://github.com/friedlanderlab/mirtrace))
-10. Present QC for raw read, alignment, and expression results ([`MultiQC`](http://multiqc.info/))
+8. Present QC for raw read, alignment, and expression results ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
-:::note
-If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-with `-profile test` before running the workflow on actual data.
-:::
+> [!NOTE]
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -89,11 +97,9 @@ nextflow run nf-core/smrnaseq \
   --outdir <OUTDIR>
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-:::
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 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).
 

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/releases/tag/dev" target="_blank">nf-core/smrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/tree/dev" target="_blank">nf-core/smrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/smrnaseq/dev/docs/output" target="_blank">documentation</a>.
+
 report_section_order:
   "nf-core-smrnaseq-methods-description":
     order: -1000

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/smrnaseq v${version} - ${runName}",
+            "author_name": "nf-core/smrnaseq ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [