From 70eb84b8d5d310c666d0de2fb5f9db401571cc39 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 9 Feb 2023 08:01:52 +0100
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
---
 conf/modules.config             | 1 +
 docs/usage.md                   | 2 +-
 subworkflows/local/profiling.nf | 3 ---
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 47c4663..b0a6e03 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -359,6 +359,7 @@ process {
     }
 
     withName: BRACKEN_BRACKEN {
+        errorStrategy = 'ignore'
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
         publishDir = [
diff --git a/docs/usage.md b/docs/usage.md
index 53dc8c3..523d92a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -103,7 +103,7 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
 motus,db_mOTU,,/<path>/<to>/motus/motus_database/
 ```
 
-For Bracken, if you wish to supply amy parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
+For Bracken, if you wish to supply any parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
 
 Column specifications are as follows:
 
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 16caa8f..cf5a9b8 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -141,7 +141,6 @@ workflow PROFILING {
 
                                     [ meta, reads, db_meta_new, db ]
                                 }
-                                .dump(tag: "ch_input_for_kraken2_after")
                                 .multiMap {
                                     it ->
                                         reads: [ it[0] + it[2], it[1] ]
@@ -184,7 +183,6 @@ workflow PROFILING {
         ch_input_for_bracken = ch_kraken2_output
             .map { meta, report -> [meta['db_name'], meta, report] }
             .combine(ch_bracken_databases, by: 0)
-            .dump(tag: "ch_input_for_bracken_b4")
             .map {
 
                 key, meta, reads, db_meta, db ->
@@ -208,7 +206,6 @@ workflow PROFILING {
 
                 [ key, meta, reads, db_meta_new, db ]
             }
-            .dump(tag: "ch_input_for_bracken_after")
             .multiMap { key, meta, report, db_meta, db ->
                 report: [meta + db_meta, report]
                 db: db