Merge pull request #435 from nf-core/dev

1.1.4 Patch release

Author: sofstam

.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"],
+        },
+    },
 }

CHANGELOG.md

@@ -3,6 +3,23 @@
 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).
 
+## v1.1.4 - Augmented Akita Patch [2024-01-24]
+
+### `Added`
+
+### `Fixed`
+
+- [#431](https://github.com/nf-core/modules/pull/4781#event-11555493525) Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
+- [#430](https://github.com/nf-core/taxprofiler/pull/430) Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)
+
+### `Dependencies`
+
+| Tool  | Previous version | New version |
+| ----- | ---------------- | ----------- |
+| kaiju | 1.8.2            | 1.10.0      |
+
+### `Deprecated`
+
 ## v1.1.3 - Augmented Akita Patch [2024-01-12]
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.1.3" target="_blank">nf-core/taxprofiler</a>
+  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.1.4" target="_blank">nf-core/taxprofiler</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/taxprofiler/1.1.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/taxprofiler/1.1.4/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-taxprofiler-methods-description":

conf/modules.config

@@ -380,7 +380,7 @@ process {
             [
                 path: { "${params.outdir}/samtools/fastq" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fastq.gz',
+                pattern: '*_other.fastq.gz',
                 enabled: params.save_hostremoval_unmapped
             ],
             [

modules.json

@@ -103,17 +103,17 @@
                     },
                     "kaiju/kaiju": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2krona": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
                         "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2table": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
                         "installed_by": ["modules"]
                     },
                     "kmcp/profile": {