Skip fastqc

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- []() - Add skip_fastqc switch to turn off FastQC reporting (by @jorondo1)
+
 - [#1006](https://github.com/nf-core/mag/pull/1006) - Add citations and references texts in the `utils_nfcore_mag_pipeline` subworkflow (by @dialvarezs)
 
 ### `Changed`

nextflow.config

@@ -29,6 +29,8 @@ params {
     adapterremoval_trim_quality_stretch  = false
     keep_phix                            = false
     skip_shortread_qc                    = false
+    skip_fastqc                          = false
+
     // long read preprocessing options
     longread_adaptertrimming_tool        = "porechop_abi"
     longread_filtering_tool              = "filtlong"

nextflow_schema.json

@@ -390,7 +390,12 @@
                 "skip_shortread_qc": {
                     "type": "boolean",
                     "description": "Skip all default QC steps for short reads (adapter trimming, phiX removal).",
-                    "help": "Skips clipping and removal of phiX sequences. Does not affect host sequence removal as this is opt in."
+                    "help": "Skips clipping and removal of phiX sequences. Does not affect host sequence removal as this is opt in. Does not prevent FastQC from running if host removal is enabled."
+                },
+                "skip_fastqc": {
+                    "type": "boolean",
+                    "description": "Skip running FastQC on short reads both before and after QC.",
+                    "help": "Skips running FastQC on short reads. Most metrics are redundant with fastp reports, but some metrics are not available in fastp. This option is useful to save time and resources when running the pipeline."
                 },
                 "save_phixremoved_reads": {
                     "type": "boolean",

subworkflows/local/preprocessing_shortread/main.nf

@@ -24,14 +24,17 @@ workflow SHORTREAD_PREPROCESSING {
     ch_host_genome_index // path(fasta)                               (optional)
     ch_phix_db_file      // [val(meta), path(fasta)]                  (optional)
     val_skip_qc          // val(boolean)
+    val_skip_fastqc      // val(boolean)
 
     main:
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
 
-    FASTQC_RAW(ch_raw_short_reads)
-    ch_versions = ch_versions.mix(FASTQC_RAW.out.versions)
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC_RAW.out.zip)
+    if (!val_skip_fastqc) {
+        FASTQC_RAW(ch_raw_short_reads)
+        ch_versions = ch_versions.mix(FASTQC_RAW.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQC_RAW.out.zip)
+    }
 
     if (!params.skip_clipping && !val_skip_qc) {
         if (params.clip_tool == 'fastp') {
@@ -148,16 +151,19 @@ workflow SHORTREAD_PREPROCESSING {
 
     /**
      * Conditions for *not* running FASTQC_TRIMMED:
-     * - No host removal and skip_qc (params.skip_shortread_qc)
+     * - Skip fastqc (params.skip_fastqc)
+     * - No host removal, skip_qc (params.skip_shortread_qc)
      * - No host removal and *both* --keep_phix --skip_clipping
      */
-    if (!(val_skip_qc && !(params.host_fasta || params.host_genome))) {
-        if (!(params.keep_phix && params.skip_clipping && !(params.host_genome || params.host_fasta))) {
-            FASTQC_TRIMMED(
-                ch_short_reads_phixremoved
-            )
-            ch_versions = ch_versions.mix(FASTQC_TRIMMED.out.versions)
-            ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMMED.out.zip)
+    if (!val_skip_fastqc) {
+        if (!(val_skip_qc && !(params.host_fasta || params.host_genome))) {
+            if (!(params.keep_phix && params.skip_clipping && !(params.host_genome || params.host_fasta))) {
+                FASTQC_TRIMMED(
+                    ch_short_reads_phixremoved
+                )
+                ch_versions = ch_versions.mix(FASTQC_TRIMMED.out.versions)
+                ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMMED.out.zip)
+            }
         }
     }
 

workflows/mag.nf

@@ -143,6 +143,7 @@ workflow MAG {
             ch_host_bowtie2index,
             ch_phix_db_file,
             params.skip_shortread_qc,
+            params.skip_fastqc,
         )
         ch_versions = ch_versions.mix(SHORTREAD_PREPROCESSING.out.versions)
         ch_multiqc_files = ch_multiqc_files.mix(