Add ability to skip fastq/falco

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - [#303](https://github.com/nf-core/taxprofiler/pull/303) Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
   - [#315](https://github.com/nf-core/taxprofiler/pull/315) Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
   - [#319](https://github.com/nf-core/taxprofiler/pull/319) Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
+  - [#323](https://github.com/nf-core/taxprofiler/pull/323) Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
 
 ### `Fixed`
 

nextflow.config

@@ -61,6 +61,7 @@ params {
     databases = null
 
     // FASTQ preprocessing
+    skip_preprocessing_qc            = false
     preprocessing_qc_tool            = 'fastqc'
 
     perform_shortread_qc             = false

nextflow_schema.json

@@ -56,6 +56,12 @@
             "description": "Common options across both long and short read preprocessing QC steps",
             "default": "",
             "properties": {
+                "skip_preprocessing_qc": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-forward",
+                    "description": "Specify to skip sequencing quality control of raw sequencing reads",
+                    "help": "Skipping running of FastQC or Falco maybe useful in cases where you are already running with preprocessed data (e.g. you are also skipping short/long read qc steps) that you already know the quality of"
+                },
                 "preprocessing_qc_tool": {
                     "type": "string",
                     "default": "fastqc",

workflows/taxprofiler.nf

@@ -144,13 +144,16 @@ workflow TAXPROFILER {
     */
     ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
 
-    if ( params.preprocessing_qc_tool == 'falco' ) {
-        FALCO ( ch_input_for_fastqc )
-        ch_versions = ch_versions.mix(FALCO.out.versions.first())
-    } else {
-        FASTQC ( ch_input_for_fastqc )
-        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    if ( !params.skip_preprocessing_qc ) {
+        if ( params.preprocessing_qc_tool == 'falco' ) {
+            FALCO ( ch_input_for_fastqc )
+            ch_versions = ch_versions.mix(FALCO.out.versions.first())
+        } else {
+            FASTQC ( ch_input_for_fastqc )
+            ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+        }
     }
+
     /*
         SUBWORKFLOW: PERFORM PREPROCESSING
     */
@@ -281,18 +284,19 @@ workflow TAXPROFILER {
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
 
-    if ( params.preprocessing_qc_tool == 'falco' ) {
-        // only mix in files actually used by MultiQC
-        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
-                            .map { meta, reports -> reports }
-                            .flatten()
-                            .filter { path -> path.name.endsWith('_data.txt')}
-                            .ifEmpty([]))
-    } else {
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    if ( !params.skip_preprocessing_qc ) {
+        if ( params.preprocessing_qc_tool == 'falco' ) {
+            // only mix in files actually used by MultiQC
+            ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
+                                .map { meta, reports -> reports }
+                                .flatten()
+                                .filter { path -> path.name.endsWith('_data.txt')}
+                                .ifEmpty([]))
+        } else {
+            ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+        }
     }
 
-
     if (params.perform_shortread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
     }