From 9bc8156ac712b2631c720a24465e252f06320795 Mon Sep 17 00:00:00 2001
From: Adam Rosenbaum <adam.rosenbaum@regionvasterbotten.se>
Date: Tue, 15 Oct 2024 10:35:37 +0200
Subject: [PATCH] Make it possible to use chopper as filtering tool as well

---
 conf/modules.config                          |  4 ++-
 nextflow.config                              |  1 -
 nextflow_schema.json                         |  8 +-----
 subworkflows/local/longread_preprocessing.nf | 29 +++++++++-----------
 4 files changed, 17 insertions(+), 25 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c3fb6a44..0adc8846 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -245,7 +245,9 @@ process {
 
     withName: CHOPPER {
         ext.args2  = [
-            "--contam ${params.lambda_reference}"
+            !params.keep_lambda ? "--contam ${params.lambda_reference}": "",
+            params.longreads_min_quality ? "--quality ${params.longreads_min_quality}": "",
+            params.longreads_min_length ? "--minlength ${params.longreads_min_length}": "",
         ].join(' ').trim()
         publishDir = [
             [
diff --git a/nextflow.config b/nextflow.config
index 822656b3..f8bf1a4e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,7 +29,6 @@ params {
     keep_phix                            = false
     // long read preprocessing options
     longread_adaptertrimming_tool        = "porechop_abi"
-    longread_phageremoval_tool           = "chopper"
     longread_filtering_tool              = "filtlong"
     // phix_reference                    = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     phix_reference                       = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6f81582e..38faad2f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -497,16 +497,10 @@
                     "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"],
+                    "enum": ["filtlong", "nanoq", "chopper"],
                     "default": "filtlong"
                 }
             }
diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
index 9e4cc0c1..76865c25 100644
--- a/subworkflows/local/longread_preprocessing.nf
+++ b/subworkflows/local/longread_preprocessing.nf
@@ -53,22 +53,13 @@ workflow LONGREAD_PREPROCESSING {
             }
         }
 
-        if (!params.keep_lambda) {
-            if (params.longread_phageremoval_tool == 'chopper') {
-                CHOPPER (
-                    ch_long_reads
-                )
-                ch_long_reads = CHOPPER.out.fastq
-                ch_versions = ch_versions.mix(CHOPPER.out.versions.first())
-            } else if (params.longread_phageremoval_tool == 'nanolyse') {
-                NANOLYSE (
-                    ch_long_reads,
-                    ch_nanolyse_db
-                )
-                ch_long_reads = NANOLYSE.out.fastq
-                ch_versions = ch_versions.mix(NANOLYSE.out.versions.first())
-            }
-
+        if (!params.keep_lambda && params.longread_filtering_tool != 'chopper') {
+            NANOLYSE (
+                ch_long_reads,
+                ch_nanolyse_db
+            )
+            ch_long_reads = NANOLYSE.out.fastq
+            ch_versions = ch_versions.mix(NANOLYSE.out.versions.first())
         }
 
         if (params.longread_filtering_tool == 'filtlong') {
@@ -95,6 +86,12 @@ workflow LONGREAD_PREPROCESSING {
             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)
+        } else if (params.longread_filtering_tool == 'chopper') {
+            CHOPPER (
+                ch_long_reads
+            )
+            ch_long_reads = CHOPPER.out.fastq
+            ch_versions = ch_versions.mix(CHOPPER.out.versions.first())
         }
 
         NANOPLOT_FILTERED (