From 80129985424b214ee22213a8db7cc139e2793ff5 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 21 Mar 2022 19:52:50 +0100
Subject: [PATCH] Make parameter naming more consistent for clipmerge

---
 conf/modules.config                           |  5 ++---
 nextflow.config                               |  6 ++---
 subworkflows/local/shortread_preprocessing.nf |  2 +-
 workflows/taxprofiler.nf                      | 22 ++++++++++++-------
 4 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 050772e..c09a011 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -41,7 +41,7 @@ process {
         // TODO also include option to NOT merge
         ext.args   = [
             { ${meta.single_end} } == 0 ? "-m" : '',
-            params.fastp_exclude_unmerged ? '' : "--include_unmerged"
+            params.shortread_excludeunmerged ? '' : "--include_unmerged"
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/fastp" },
@@ -84,7 +84,7 @@ process {
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.when = params.run_malt
+        ext.prefix = { "${meta.id}-${meta.db_name}" }
     }
 
     withName: KRAKEN2_KRAKEN2 {
@@ -94,7 +94,6 @@ process {
             pattern: '.{fastq.gz,txt}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.when = params.run_kraken2
         ext.prefix = { "${meta.id}-${meta.db_name}" }
     }
 
diff --git a/nextflow.config b/nextflow.config
index 4a3a56d..5f7aec6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -55,9 +55,9 @@ params {
     databases = null
 
     // FASTQ preprocessing
-    fastp_clip_merge           = false
-    fastp_exclude_unmerged     = true
-    remove_adapters            = false
+    shortread_clipmerge           = false
+    shortread_excludeunmerged        = true
+    longread_clip                 = false
 
     // MALT
     run_malt                   = false
diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf
index 406c198..d996a76 100644
--- a/subworkflows/local/shortread_preprocessing.nf
+++ b/subworkflows/local/shortread_preprocessing.nf
@@ -23,7 +23,7 @@ workflow SHORTREAD_PREPROCESSING {
     // TODO move to subworkflow
 
 
-    if ( params.fastp_clip_merge ) {
+    if ( params.shortread_clipmerge ) {
 
         ch_input_for_fastp = reads
                                 .dump(tag: "pre-fastp_branch")
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 22c7518..4aa0684 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -100,17 +100,14 @@ workflow TAXPROFILER {
     //
     // PERFORM PREPROCESSING
     //
-    if ( params.fastp_clip_merge ) {
+    if ( params.shortread_clipmerge ) {
         SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
     }
 
-    ch_multiqc_files = Channel.empty()
-
-    if ( params.remove_adapters ) {
+    if ( params.longread_clip ) {
         ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
                                         .map { it -> [ it[0], [it[1]] ] }
     ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
-        ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
     } else {
         ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
     }
@@ -187,9 +184,13 @@ workflow TAXPROFILER {
     //
     // RUN PROFILING
     //
-    MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
-    KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db  )
+    if ( params.run_malt ) {
+        MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
+    }
 
+    if ( params.run_kraken2 ) {
+        KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db  )
+    }
 
     //
     // MODULE: MultiQC
@@ -197,14 +198,19 @@ workflow TAXPROFILER {
     workflow_summary    = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
     ch_workflow_summary = Channel.value(workflow_summary)
 
+    ch_multiqc_files = Channel.empty()
     ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
     ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-    if (params.fastp_clip_merge) {
+
+    if (params.shortread_clipmerge) {
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
     }
+    if (params.longread_clip) {
+        ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
+    }
     if (params.run_kraken2) {
         ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))
         ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())