Merge pull request #430 from nf-core/samtools_fastq

Fix the multiple fastq outputs in LONGREAD_HOSTREMOVAL

.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

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#430](https://github.com/nf-core/taxprofiler/pull/430) Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)
+
 ### `Dependencies`
 
 ### `Deprecated`

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
             ],
             [

subworkflows/local/longread_hostremoval.nf

@@ -54,7 +54,7 @@ workflow LONGREAD_HOSTREMOVAL {
 
     emit:
     stats    = SAMTOOLS_STATS.out.stats     //channel: [val(meta), [reads  ] ]
-    reads    = SAMTOOLS_FASTQ.out.fastq.mix( SAMTOOLS_FASTQ.out.other)   // channel: [ val(meta), [ reads ] ]
+    reads    = SAMTOOLS_FASTQ.out.other   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions                 // channel: [ versions.yml ]
     mqc      = ch_multiqc_files
 }