Merge pull request #70 from YiJin-Xiong/YiJin-Xiong-patch-2

Update V2.0.0

Author: YiJin-Xiong

.github/workflows/ci.yml

@@ -41,7 +41,7 @@ jobs:
           - "--reset"
           - "--skip_snvs"
           - "--haplotype_dmrer dss"
-          - "--m6a"
+          - "--fiberseq"
         profile:
           #- "conda"
           - "docker"

.nf-test.log

@@ -0,0 +1,18 @@
+Oct-30 15:30:57.200 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.3
+Oct-30 15:30:57.219 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test, --profile=+singularity, --updateSnapshot]
+Oct-30 15:30:58.828 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 25.04.2
+Oct-30 15:30:58.832 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong/nf-test.config...
+Oct-30 15:31:00.162 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 68 files from directory /dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong in 0.755 sec
+Oct-30 15:31:00.163 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
+Oct-30 15:31:00.164 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong/tests/default.nf.test]
+Oct-30 15:31:00.721 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
+Oct-30 15:31:00.722 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+Oct-30 15:31:00.723 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test pipeline' from file '/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong/tests/default.nf.test'.
+Oct-30 15:31:00.723 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '4a8ebd5b: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+Oct-30 15:44:15.752 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong/tests/default.nf.test.snap'
+Oct-30 15:44:16.017 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots '-profile test' do not match. Update snapshots flag set.
+Oct-30 15:44:16.017 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot '-profile test'
+Oct-30 15:44:16.235 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/Jin/methylong_pull_request/PR_v2/methylong/tests/default.nf.test.snap'
+Oct-30 15:44:16.236 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '4a8ebd5b: -profile test' finished. status: PASSED
+Oct-30 15:44:16.239 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: true, skipped tests: false, failed tests: false
+Oct-30 15:44:16.242 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

.nf-test/plugins/769ef9cb3e09a5479af8ae24f9f6ea54.json

@@ -0,0 +1,158 @@
+[{
+  "id": "nft-fasta",
+  "latest": "1.0.0",
+  "url": "https://github.com/askimed/nft-fasta",
+  "github": "askimed/nft-fasta",
+  "description": "Provides support for FASTA files.",
+  "author": "Lukas Forer",
+  "keywords": [],
+  "releases": [{
+    "version": "1.0.0",
+    "url": "https://github.com/askimed/nft-fasta/releases/download/v1.0.0/nft-fasta-1.0.0.jar"
+  }]
+},{
+  "id": "nft-vcf",
+  "latest": "1.0.7",
+  "url": "https://github.com/seppinho/nft-vcf",
+  "github": "seppinho/nft-vcf",
+  "description": "Provides support for VCF files.",
+  "author": "Sebastian Schönherr",
+  "keywords": [],
+  "releases": [{
+    "version": "1.0.2",
+    "url": "https://github.com/seppinho/nft-vcf/releases/download/v1.0.2/nft-vcf-1.0.2-jar-with-dependencies.jar"
+  },{
+    "version": "1.0.4",
+    "url": "https://github.com/seppinho/nft-vcf/releases/download/v1.0.4/nft-vcf-1.0.4.jar"
+  },{
+    "version": "1.0.5",
+    "url": "https://github.com/seppinho/nft-vcf/releases/download/v1.0.5/nft-vcf-1.0.5.jar"
+  },{
+    "version": "1.0.6",
+    "url": "https://github.com/seppinho/nft-vcf/releases/download/v1.0.6/nft-vcf-1.0.6.jar"
+  },{
+    "version": "1.0.7",
+    "url": "https://github.com/seppinho/nft-vcf/releases/download/v1.0.7/nft-vcf-1.0.7.jar"
+  }]
+},{
+  "id": "nft-bam",
+  "latest": "0.6.0",
+  "url": "https://nvnieuwk.github.io/nft-bam",
+  "github": "nvnieuwk/nft-bam",
+  "description": "Provides some helper functionality for handling SAM/BAM/CRAM files during tests",
+  "author": "Nicolas Vannieuwkerke",
+  "keywords": [],
+  "releases": [{
+    "version": "0.1.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.1.0/nft-bam-0.1.0.jar"
+  },{
+    "version": "0.1.1",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.1.1/nft-bam-0.1.1.jar"
+  },{
+    "version": "0.2.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.2.0/nft-bam-0.2.0.jar"
+  },{
+    "version": "0.3.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.3.0/nft-bam-0.3.0.jar"
+  },{
+    "version": "0.4.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.4.0/nft-bam-0.4.0.jar"
+  },{
+    "version": "0.5.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.5.0/nft-bam-0.5.0.jar"
+  },{
+    "version": "0.6.0",
+    "url": "https://github.com/nvnieuwk/nft-bam/releases/download/0.6.0/nft-bam-0.6.0.jar"
+  }]
+},{
+  "id": "nft-compress",
+  "latest": "0.1.0",
+  "url": "https://github.com/lukfor/nft-compress",
+  "github": "lukfor/nft-compress",
+  "description": "Provides support for ZIP files.",
+  "author": "Lukas Forer",
+  "keywords": [],
+  "releases": [{
+    "version": "0.1.0",
+    "url": "https://github.com/lukfor/nft-compress/releases/download/0.1.0/nft-compress-0.1.0.jar"
+  }]
+},{
+  "id": "nft-csv",
+  "latest": "0.1.0",
+  "url": "https://github.com/lukfor/nft-csv",
+  "github": "lukfor/nft-csv",
+  "description": "Provides support for CSV files.",
+  "author": "Lukas Forer",
+  "keywords": [],
+  "releases": [{
+    "version": "0.1.0",
+    "url": "https://github.com/lukfor/nft-csv/releases/download/0.1.0/nft-csv-0.1.0.jar"
+  }]
+},{
+  "id": "nft-utils",
+  "latest": "0.0.7",
+  "url": "https://github.com/nf-core/nft-utils",
+  "github": "nf-core/nft-utils",
+  "description": "nf-test utility functions for Nextflow pipelines.",
+  "author": "nf-core",
+  "keywords": [],
+  "releases": [{
+    "version": "0.0.1",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.1/nft-utils-0.0.1.jar"
+  },{
+    "version": "0.0.2",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.2/nft-utils-0.0.2.jar"
+  },{
+    "version": "0.0.3",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.3/nft-utils-0.0.3.jar"
+  },{
+    "version": "0.0.4",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.4/nft-utils-0.0.4.jar"
+  },{
+    "version": "0.0.5",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.5/nft-utils-0.0.5.jar"
+  },{
+    "version": "0.0.6",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.6/nft-utils-0.0.6.jar"
+  },{
+    "version": "0.0.7",
+    "url": "https://github.com/nf-core/nft-utils/releases/download/0.0.7/nft-utils-0.0.7.jar"
+  }]
+},{
+  "id": "nft-fastq",
+  "latest": "0.0.1",
+  "url": "https://github.com/lukfor/nft-fastq",
+  "github": "lukfor/nft-fastq",
+  "description": "Provides support for FASTQ files.",
+  "author": "Lukas Forer",
+  "keywords": [],
+  "releases": [{
+    "version": "0.0.1",
+    "url": "https://github.com/lukfor/nft-fastq/releases/download/v0.0.1/nft-fastq-0.0.1-all.jar"
+  }]
+}, {
+  "id": "nft-anndata",
+  "latest": "0.1.0",
+  "url": "https://github.com/nictru/nft-anndata",
+  "github": "nictru/nft-anndata",
+  "description": "Provides support for AnnData (h5ad) files.",
+  "author": "Nico Trummer",
+  "keywords": [],
+  "releases": [{
+    "version": "0.1.0",
+    "url": "https://github.com/nictru/nft-anndata/releases/download/v0.1.0/nft-anndata-0.1.0.jar"
+  }]
+}, {
+  "id": "nft-tiff",
+  "latest": "0.1.0",
+  "url": "https://github.com/nf-core/nft-tiff",
+  "github": "nf-core/nft-tiff",
+  "description": "Provides support for TIFF files.",
+  "author": "nf-core",
+  "keywords": [],
+  "releases": [{
+    "version": "0.1.0",
+    "url": "https://github.com/nf-core/nft-tiff/releases/download/v0.1.0/nft-tiff-0.1.0.jar"
+  }]
+}
+]

.nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar

@@ -12,3 +12,4 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/**/meta.yml

.nf-test/plugins/nft-utils/0.0.7/nft-utils-0.0.7.jar

@@ -14,19 +14,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `fibertools` modules for m6A call
 - Change the input samplesheet structure
 
-### `Fixed`
-
 ### `Dependencies`
 
 | Dependency   | Old version | New version |
 | ------------ | ----------- | ----------- |
-| `dorado`     |             | 0.9.5       |
+| `dorado`     | 0.9.5       | 1.1.1       |
 | `jasmine`    |             | 2.4.0       |
 | `ccsmeth`    |             | 0.5.0       |
 | `DSS`        |             | 2.54.0      |
 | `fibertools` |             | 0.6.4       |
+| `modkit`     | 0.4.4       | 0.5.0       |
+| `samtools`   | 1.21        | 1.22.1      |
 
-### `Deprecated`
+### Requirements
+
+- Nextflow `>=25.04.0`
+
+### Contributors
+
+- @YiJin-Xiong for implementing `fiberseq`, `dmr calling` subworkflows.
+- @jkh00 for code review, suggestions and template updates.
 
 ## v1.1.0 - [2025-05-28]
 
@@ -47,7 +54,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `whatshap` |             | 2.6         |
 | `gawk`     |             | 5.3.0       |
 
-### `Deprecated`
+### New Contributors
+
+- New subworkflows were created by @YiJin-Xiong
 
 ## v1.0.0 'Niveous Tiger' - [2025-05-08]
 
@@ -60,3 +69,7 @@ Initial release of nf-core/methylong, created with the [nf-core](https://nf-co.r
 ### `Dependencies`
 
 ### `Deprecated`
+
+### Credits
+
+- special thanks to @fellen31 for valuable code review and feedback on the pipeline structure.

.nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar

@@ -32,7 +32,6 @@
 
 1. modcalling (optional)
    - basecall pod5 reads to modBam - `dorado basecaller`
-   - optional: m6A call - `fibertools add-nucleosomes`
 2. trim and repair tags of input modBam
    - trim and repair workflow:
      1. sort modBam - `samtools sort`
@@ -45,14 +44,12 @@
    - include alignment summary - `samtools flagstat`
 
 4. create bedMethyl - `modkit pileup`, 5x base coverage minimum.
-   - optional: extract m6A information into bedMethyl - `fibertools extract`
 5. create bedgraphs (optional)
 
 ### PacBio workflow:
 
 1. modcalling (optional)
    - modcall bam reads to modBam - `jasmine` (default) or `ccsmeth`
-   - optional: m6A call - `fibertools predict-m6a`
 
 2. align to reference - `pbmm2` (default) or `minimap2`
    - minimap workflow:
@@ -74,8 +71,6 @@
        2. or `count` (differences described here: https://github.com/PacificBiosciences/pb-CpG-tools)
      - `pb-CpG-tools` by default merge mC signals on CpG into forward strand. To 'force' strand specific signal output, I followed the suggestion mentioned in this issue ([PacificBiosciences/pb-CpG-tools#37](https://github.com/PacificBiosciences/pb-CpG-tools/issues/37)) which uses HP tags to tag forward and reverse reads, so they were output separately.
 
-   - optional: extract m6A information into bedMethyl - `fibertools extract`
-
 4. create bedgraph (optional)
 
 ### Downstream workflow:
@@ -87,6 +82,17 @@
      1. tag reads by haplotype - `whatshap haplotype`
      2. create bedMethyl - `modkit pileup`
      3. DMR - `DSS` (default) or `modkit dmr`
+        - in `DSS` , regions with statistically significant CpG sites will be detected as DMRs.
+
+### Fiberseq workflow:
+
+- ONT alignedBAM
+  1. filtering m6A calls - `modkit call-mods`
+  2. infer nucleosomes and MSPs - `ft add-nuleosomes`
+  3. create bedMethyl - `ft extract`
+- PacBio alignedBAM
+  1. predict m6a and infer nucleosomes - `ft predict-m6a`
+  2. create bedMethyl - `ft extract`
 
 ## Usage
 
@@ -155,6 +161,10 @@ Folder stuctures of the outputs:
 │   ├── basecall
 │   │   └── calls.bam
 │   │
+│   ├── fiberseq
+│   │   ├── m6acall.bam
+│   │   └── m6a.bed
+│   │
 │   ├── trim
 │   │   ├── trimmed.fastq.gz
 │   │   └── trimmed.log
@@ -204,7 +214,9 @@ Folder stuctures of the outputs:
 │   ├── fastqc
 │   │
 │   ├── modcall
-│   │   ├── modbam.bam
+│   │   └── modbam.bam
+│   │
+│   ├── fiberseq
 │   │   ├── m6a_predicted.bam
 │   │   └── m6a.bed
 │   │
@@ -274,12 +286,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-
 If you use nf-core/methylong for your analysis, please cite it using the following doi: [10.5281/zenodo.15366448](https://doi.org/10.5281/zenodo.15366448)
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

.prettierignore

@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/methylong/releases/tag/1.0.0" target="_blank">nf-core/methylong</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/methylong/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/methylong/releases/tag/2.0.0" target="_blank">nf-core/methylong</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/methylong/2.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylong-methods-description":
     order: -1000