nf-core · jfy133 · Jun 20, 2025 · Jun 12, 2025 · Jun 13, 2025 · Jun 13, 2025
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#718](https://github.com/nf-core/mag/pull/718) - Added metaMDBG and (meta)Flye as long read assemblers (added by @muabnezor)
 - [#718](https://github.com/nf-core/mag/pull/718) - Added host removal for long reads using minimap2 as aligner (added by @muabnezor)
 - [#827](https://github.com/nf-core/mag/pull/827) - Added nf-test CI testing for all test profiles (added by @jfy133)
+- [#829](https://github.com/nf-core/mag/pull/829) - Add `--skip_shortread_qc` and `--skip_longread_qc` params for skipping certain default preprocessing steps (added by @erikrikarddaniel)
 
 ### `Changed`
 

@@ -28,6 +28,7 @@ params {
     adapterremoval_adapter2              = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
     adapterremoval_trim_quality_stretch  = false
     keep_phix                            = false
+    skip_shortread_qc                    = false
     // long read preprocessing options
     longread_adaptertrimming_tool        = "porechop_abi"
     longread_filtering_tool              = "filtlong"
@@ -108,6 +109,7 @@ params {
     // long read preprocessing options
     skip_adapter_trimming                = false
     skip_longread_filtering              = false
+    skip_longread_qc                     = false
     keep_lambda                          = false
     longreads_min_quality                = null
     longreads_min_length                 = 1000

@@ -376,6 +376,11 @@
                     "type": "boolean",
                     "description": "Skip read preprocessing using fastp or adapterremoval."
                 },
+                "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."
+                },
                 "save_phixremoved_reads": {
                     "type": "boolean",
                     "description": "Specify to save input FASTQ files with phiX reads removed to --outdir."
@@ -414,6 +419,11 @@
                     "type": "boolean",
                     "description": "Skip filtering long reads."
                 },
+                "skip_longread_qc": {
+                    "type": "boolean",
+                    "description": "Skip all default QC steps for long reads (adapter trimming, filtering, removal of lambda sequences).",
+                    "help": "Skips adapter trimming and filtering, but not host sequence removal."
+                },
                 "longreads_min_length": {
                     "type": "integer",
                     "default": 1000,

@@ -21,6 +21,7 @@ workflow LONGREAD_PREPROCESSING {
     ch_short_reads            // [ [meta] , fastq1, fastq2] (mandatory)
     ch_lambda_db              // [fasta]
     ch_host_fasta             // [fasta]
+    skip_qc                   // [boolean]
 
     main:
     ch_versions = Channel.empty()
@@ -32,7 +33,7 @@ workflow LONGREAD_PREPROCESSING {
     ch_versions = ch_versions.mix(NANOPLOT_RAW.out.versions.first())
 
     if ( !params.assembly_input ) {
-        if (!params.skip_adapter_trimming) {
+        if (!params.skip_adapter_trimming && !skip_qc) {
             if (params.longread_adaptertrimming_tool &&
                 params.longread_adaptertrimming_tool == 'porechop_abi') {
                 PORECHOP_ABI (
@@ -53,15 +54,15 @@ workflow LONGREAD_PREPROCESSING {
             ch_long_reads = ch_raw_long_reads
         }
 
-        if (!params.keep_lambda && params.longread_filtering_tool != 'chopper') {
+        if (!params.keep_lambda && params.longread_filtering_tool != 'chopper' && !skip_qc) {
             NANOLYSE (
                 ch_long_reads,
                 ch_lambda_db
             )
             ch_long_reads = NANOLYSE.out.fastq
             ch_versions = ch_versions.mix(NANOLYSE.out.versions.first())
         }
-        if (!params.skip_longread_filtering) {
+        if (!params.skip_longread_filtering && !skip_qc) {
             if (params.longread_filtering_tool == 'filtlong') {
                 // join long and short reads by sample name
                 ch_short_reads_tmp = ch_short_reads
@@ -108,16 +109,23 @@ workflow LONGREAD_PREPROCESSING {
             ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_HOSTREMOVAL.out.multiqc_files )
         }
 
-        if (!(
-            params.skip_adapter_trimming &&
-            params.skip_longread_filtering &&
-            !params.host_fasta &&
-            params.keep_lambda
-        )) {
-            NANOPLOT_FILTERED (
-                ch_long_reads
-            )
-            ch_versions = ch_versions.mix(NANOPLOT_FILTERED.out.versions.first())
+        /**
+         * Conditions for *not* running NANOPLOT_FILTERED:
+         * - No host removal and skip_qc (params.skip_longread_qc)
+         * - No host removal and *all* --keep_lambda, --skip_adapter_trimming, --skip_longread_filtering
+         */
+        if ( !( ( skip_qc && !( params.host_fasta || params.host_genome ) ) ) ) {
+            if (
+                !(
+                    params.skip_adapter_trimming && params.skip_longread_filtering && params.keep_lambda &&
+                    !(params.host_fasta || params.host_genome )
+                )
+            ) {
+                NANOPLOT_FILTERED (
+                    ch_long_reads
+                )
+                ch_versions = ch_versions.mix(NANOPLOT_FILTERED.out.versions.first())
+            }
         }
 
         // Run merging

@@ -22,6 +22,7 @@ workflow SHORTREAD_PREPROCESSING {
     ch_host_fasta        // [fasta] (optional)
     ch_host_genome_index // fasta (optional)
     ch_phix_db_file      // [fasta] (optional)
+    skip_qc              // [boolean]
 
     main:
     ch_versions = Channel.empty()
@@ -33,7 +34,7 @@ workflow SHORTREAD_PREPROCESSING {
     ch_versions = ch_versions.mix(FASTQC_RAW.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC_RAW.out.zip)
 
-    if (!params.skip_clipping) {
+    if (!params.skip_clipping && !skip_qc) {
         if (params.clip_tool == 'fastp') {
             FASTP(
                 ch_raw_short_reads,
@@ -111,7 +112,7 @@ workflow SHORTREAD_PREPROCESSING {
         ch_short_reads_hostremoved = ch_short_reads_prepped
     }
 
-    if (!params.keep_phix) {
+    if (!params.keep_phix && !skip_qc) {
         ch_phix_fasta_for_build = ch_phix_db_file.combine(ch_short_reads_prepped)
                 .map { host_fasta, meta, reads ->
                     host_fasta
@@ -131,12 +132,24 @@ workflow SHORTREAD_PREPROCESSING {
         ch_short_reads_phixremoved = ch_short_reads_hostremoved
     }
 
-    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)
+    /**
+     * Conditions for *not* running FASTQC_TRIMMED:
+     * - No host removal and skip_qc (params.skip_shortread_qc)
+     * - No host removal and *both* --keep_phix --skip_clipping
+     */
+    if ( !( ( 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)
+        }
     }
 
     // Run/Lane merging

@@ -136,6 +136,7 @@ workflow MAG {
             ch_host_fasta,
             ch_host_bowtie2index,
             ch_phix_db_file,
+            params.skip_shortread_qc,
         )
 
         ch_versions = ch_versions.mix(SHORTREAD_PREPROCESSING.out.versions)
@@ -161,6 +162,7 @@ workflow MAG {
         ch_short_reads,
         ch_lambda_db,
         ch_host_fasta,
+        params.skip_longread_qc,
     )
 
     ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions)