From c8f6d713a34ab90db60210972020b5be53e82d45 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 16 Jan 2023 14:49:44 +0100
Subject: [PATCH] Add tool names to end of prefix files for easier
 distinguishing in general stats

---
 conf/modules.config | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5920a58..ca4d9b3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -350,7 +350,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -389,7 +389,7 @@ process {
     withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         ext.args = { "${meta.db_params}" }
         // one run with multiple samples, so fix ID to just db name to ensure clean log name
-        ext.prefix = { "${meta.db_name}" }
+        ext.prefix = { "${meta.db_name}.krakenuniq" }
         publishDir = [
             path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -432,7 +432,7 @@ process {
 
     withName: METAPHLAN3_METAPHLAN3 {
         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}.metaphlan3" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.metaphlan3" }
         publishDir = [
             path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -480,7 +480,7 @@ process {
     }
 
     withName: KAIJU_KAIJU {
-        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}-${meta.db_name}.kaiju" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kaiju" }
         publishDir = [
             path: { "${params.outdir}/kaiju/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -504,7 +504,7 @@ process {
 
     withName: DIAMOND_BLASTX {
         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}.diamond" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.diamond" }
         publishDir = [
             path: { "${params.outdir}/diamond/${meta.db_name}/" },
             mode: params.publish_dir_mode,