Add helptest to nextflow_schema,add versions to longread_preprocessing

.github/workflows/ci.yml

@@ -23,7 +23,6 @@ jobs:
           - "21.10.3"
           - "latest-everything"
         parameters:
-          - "--preprocessing_qc_tool fastqc"
           - "--preprocessing_qc_tool falco"
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"

docs/usage.md

@@ -168,7 +168,7 @@ work                # Directory containing the nextflow working files
 
 ### Sequencing quality control
 
-nf-core taxprofiler offers [`Falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
 
 ### Preprocessing Steps
 

nextflow_schema.json

@@ -712,7 +712,9 @@
         "preprocessing_qc_tool": {
             "type": "string",
             "default": "fastqc",
-            "enum": ["fastqc", "falco"]
+            "enum": ["fastqc", "falco"],
+            "help_text": "Falco is aimed at being a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
+            "description": "By default, the pipeline utilizes FastQC tool for quality control of raw sequencing reads"
         }
     }
 }

subworkflows/local/longread_preprocessing.nf

@@ -56,10 +56,12 @@ workflow LONGREAD_PREPROCESSING {
 
     if (params.preprocessing_qc_tool == 'fastqc') {
         FASTQC_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
 
     } else if (params.preprocessing_qc_tool == 'falco') {
         FALCO_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
     }