Merge pull request #5 from jkh00/bump_version

Update version & changelog

Author: YiJin-Xiong

.nf-test.log

@@ -1,18 +1,18 @@
-Oct-30 11:47:26.905 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.3
-Oct-30 11:47:26.939 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test, --profile=+singularity, --updateSnapshot]
-Oct-30 11:47:28.563 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 25.04.2
-Oct-30 11:47:28.566 [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 11:47:30.443 [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 0.991 sec
-Oct-30 11:47:30.446 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
-Oct-30 11:47:30.447 [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 11:47:31.011 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
-Oct-30 11:47:31.012 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
-Oct-30 11:47:31.013 [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 11:47:31.013 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '4a8ebd5b: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
-Oct-30 12:00:34.573 [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 12:00:34.965 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots '-profile test' do not match. Update snapshots flag set.
-Oct-30 12:00:34.966 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot '-profile test'
-Oct-30 12:00:35.188 [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 12:00:35.189 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '4a8ebd5b: -profile test' finished. status: PASSED
-Oct-30 12:00:35.192 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: true, skipped tests: false, failed tests: false
-Oct-30 12:00:35.194 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!
+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!

CHANGELOG.md

@@ -14,8 +14,6 @@ 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 |
@@ -28,7 +26,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `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]
 
@@ -49,7 +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]
 
@@ -62,3 +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.

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/methylong/releases/tag/2" 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/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

nextflow.config

@@ -284,7 +284,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.04.0'
-    version         = '2'
+    version         = '2.0.0'
     doi             = '10.5281/zenodo.15366449'
 }