From e76b299705152e6ef3015658507cf78213818194 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 26 Jul 2022 08:18:54 +0000
Subject: [PATCH] Start working getting kraken and centrifuge working in MQC

---
 assets/multiqc_config.yml       | 32 ++++++++++++++++++++++++++++++++
 conf/modules.config             |  6 +++---
 subworkflows/local/profiling.nf |  3 ++-
 3 files changed, 37 insertions(+), 4 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 438fb42..00e09c5 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -13,3 +13,35 @@ export_plots: true
 custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
 custom_logo_url: https://nf-co.re/taxprofiler
 custom_logo_title: "nf-core/taxprofiler"
+
+run_modules:
+    - fastqc
+    - adapterRemoval
+    - fastp
+    - bowtie2
+    - kraken
+    - malt
+
+#extra_fn_clean_exts:
+#    - '_fastp'
+#    - '.pe.settings'
+#    - '.se.settings'
+
+top_modules:
+  - 'fastqc':
+    name: "FastQC (pre-processing)"
+    path_filters:
+      - '*_raw.zip'
+  - 'fastp'
+  - 'fastqc':
+    name: "FastQC (post-processing)"
+    path_filters:
+      - '*_processed.zip'
+  - 'kraken':
+    name: "Kraken"
+    path_filters:
+      - '*kraken.report'
+  - 'kraken':
+    name: Centrifuge"
+    path_filters:
+      - '*centrifuge.kreport'
diff --git a/conf/modules.config b/conf/modules.config
index 1558a98..ea2f487 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -285,7 +285,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kraken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: params.publish_dir_mode,
@@ -343,12 +343,12 @@ process {
             pattern: '*.{txt,sam,gz}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
     }
 
     withName: CENTRIFUGE_KREPORT {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}" },
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 7c2c90c..921f291 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -127,7 +127,7 @@ workflow PROFILING {
                                 }
 
         KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
-        ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([])  )
+        ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report  )
         ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
         ch_raw_profiles        = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
@@ -152,6 +152,7 @@ workflow PROFILING {
         ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
         ch_raw_profiles        = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
+        ch_multiqc_files       = ch_multiqc_files.mix( CENTRIFUGE_KREPORT.out.kreport )
 
     }