Fix config for modules nanoq and filtlong in modules.config

nf-core · Oct 14, 2024 · 7102af4 · 7102af4
1 parent c614c01
commit 7102af4
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Showing 4 changed files with 79 additions and 14 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -192,17 +192,40 @@ process {
             "--min_length ${params.longreads_min_length}",
             "--keep_percent ${params.longreads_keep_percent}",
             "--trim",
-            "--length_weight ${params.longreads_length_weight}"
+            "--length_weight ${params.longreads_length_weight}",
+            params.longreads_min_quality ? "--min_mean_q ${params.longreads_min_quality}" : '',
         ].join(' ').trim()
         publishDir = [
                 path: { "${params.outdir}/QC_longreads/Filtlong" },
                 mode: params.publish_dir_mode,
                 pattern: "*_filtlong.fastq.gz",
-                enabled: params.save_filtlong_reads
+                enabled: params.save_filtered_reads
             ]
         ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
     }
 
+    withName: NANOQ {
+        ext.args = [
+            "--min-len ${params.longreads_min_length}",
+            params.longreads_min_quality ? "--min-qual ${params.longreads_min_quality}": '',
+            "-vv"
+        ].join(' ').trim()
+        publishDir = [
+            [
+            path: { "${params.outdir}/QC_longreads/Nanoq" },
+            mode: params.publish_dir_mode,
+            pattern: "*_nanoq_filtered.fastq.gz",
+            enabled: params.save_filtered_reads
+            ],
+            [
+                path: { "${params.outdir}/QC_longreads/Nanoq" },
+                mode: params.publish_dir_mode,
+                pattern: "*_nanoq_filtered.stats"
+            ]
+        ]
+        ext.prefix = { "${meta.id}_run${meta.run}_nanoq_filtered" }
+    }
+
     withName: NANOLYSE {
         publishDir = [
             [
@@ -220,6 +243,26 @@ process {
         ext.prefix = { "${meta.id}_run${meta.run}_lambdafiltered" }
     }
 
+    withName: CHOPPER {
+        ext.args2  = [
+            "--contam ${params.lambda_reference}"
+        ].join(' ').trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/QC_longreads/Chopper" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/QC_longreads/Chopper" },
+                mode: params.publish_dir_mode,
+                pattern: "*_chopper.fastq.gz",
+                enabled: params.save_lambdaremoved_reads
+            ]
+        ]
+        ext.prefix =  { "${meta.id}_run${meta.run}_chopper" }
+    }
+
     withName: NANOPLOT_RAW {
         ext.prefix = 'raw'
         ext.args   = {

diff --git a/nextflow.config b/nextflow.config
@@ -28,7 +28,9 @@ params {
     adapterremoval_trim_quality_stretch  = false
     keep_phix                            = false
     // long read preprocessing options
-    longread_adaptertrimming_tool         = "porechop_abi"
+    longread_adaptertrimming_tool        = "porechop_abi"
+    longread_phageremoval_tool           = "chopper"
+    longread_filtering_tool              = "filtlong"
     // phix_reference                    = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     phix_reference                       = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     save_phixremoved_reads               = false
@@ -102,14 +104,15 @@ params {
     // long read preprocessing options
     skip_adapter_trimming                = false
     keep_lambda                          = false
+    longreads_min_quality                = null
     longreads_min_length                 = 1000
     longreads_keep_percent               = 90
     longreads_length_weight              = 10
     // lambda_reference                  = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Escherichia_virus_Lambda/all_assembly_versions/GCA_000840245.1_ViralProj14204/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
     lambda_reference                     = "${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
     save_lambdaremoved_reads             = false
     save_porechop_reads                  = false
-    save_filtlong_reads                  = false
+    save_filtered_reads                  = false
 
     // binning options
     skip_metabat2                   = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -453,6 +453,11 @@
                     "default": 1000,
                     "description": "Discard any read which is shorter than this value."
                 },
+                "longreads_min_quality": {
+                    "type": "integer",
+                    "default": null,
+                    "description": "Discard any read which has a mean quality score lower than this value."
+                },
                 "longreads_keep_percent": {
                     "type": "integer",
                     "default": 90,
@@ -482,7 +487,7 @@
                     "type": "boolean",
                     "description": "Specify to save the resulting clipped FASTQ files to --outdir."
                 },
-                "save_filtlong_reads": {
+                "save_filtered_reads": {
                     "type": "boolean",
                     "description": "Specify to save the resulting length filtered FASTQ files to --outdir."
                 },
@@ -491,6 +496,18 @@
                     "description": "Specify which long read adapter trimming tool to use.",
                     "enum": ["porechop", "porechop_abi"],
                     "default": "porechop_abi"
+                },
+                "longread_phageremoval_tool": {
+                    "type": "string",
+                    "description": "Specify which long read phage removal tool to use.",
+                    "enum": ["nanolyse", "chopper"],
+                    "default": "chopper"
+                },
+                "longread_filtering_tool": {
+                    "type": "string",
+                    "description": "Specify which long read filtering tool to use.",
+                    "enum": ["filtlong", "nanoq"],
+                    "default": "filtlong"
                 }
             }
         },

diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
@@ -71,16 +71,16 @@ workflow LONGREAD_PREPROCESSING {
 
         }
 
-        // join long and short reads by sample name
-        ch_short_reads_tmp = ch_short_reads
-            .map { meta, sr -> [ meta.id, meta, sr ] }
+        if (params.longread_filtering_tool == 'filtlong') {
+            // join long and short reads by sample name
+            ch_short_reads_tmp = ch_short_reads
+                .map { meta, sr -> [ meta.id, meta, sr ] }
 
-        ch_short_and_long_reads = ch_long_reads
-            .map { meta, lr -> [ meta.id, meta, lr ] }
-            .join(ch_short_reads_tmp, by: 0)
-            .map { id, meta_lr, lr, meta_sr, sr -> [ meta_lr, sr, lr ] }  // should not occur for single-end, since SPAdes (hybrid) does not support single-end
+            ch_short_and_long_reads = ch_long_reads
+                .map { meta, lr -> [ meta.id, meta, lr ] }
+                .join(ch_short_reads_tmp, by: 0)
+                .map { id, meta_lr, lr, meta_sr, sr -> [ meta_lr, sr, lr ] }  // should not occur for single-end, since SPAdes (hybrid) does not support single-end
 
-        if (params.longread_filtering_tool == 'filtlong') {
             FILTLONG (
                 ch_short_and_long_reads
             )
@@ -89,10 +89,12 @@ workflow LONGREAD_PREPROCESSING {
             ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
         } else if (params.longread_filtering_tool == 'nanoq') {
             NANOQ (
-                ch_long_reads
+                ch_long_reads,
+                'fastq.gz'
             )
             ch_long_reads = NANOQ.out.reads
             ch_versions = ch_versions.mix(NANOQ.out.versions.first())
+            ch_multiqc_files = ch_multiqc_files.mix(NANOQ.out.stats)
         }
 
         NANOPLOT_FILTERED (