From aa687975c842f74cb4ba2d7c94f66cdcc24b8b37 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 30 Aug 2022 15:15:48 +0200
Subject: [PATCH] Update bracken (#1982)

* chore: update version

* tests: update use of kraken2 module
---
 modules/bracken/bracken/main.nf        | 14 +++++++++-----
 tests/modules/bracken/bracken/main.nf  | 16 ++++++++--------
 tests/modules/bracken/bracken/test.yml |  8 ++++----
 3 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/modules/bracken/bracken/main.nf b/modules/bracken/bracken/main.nf
index 2027fd23eb38..5e08418966da 100644
--- a/modules/bracken/bracken/main.nf
+++ b/modules/bracken/bracken/main.nf
@@ -2,10 +2,12 @@ process BRACKEN_BRACKEN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bracken=2.6.2" : null)
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bracken:2.6.2--py39hc16433a_0':
-        'quay.io/biocontainers/bracken:2.6.2--py39hc16433a_0' }"
+        'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
+        'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
 
     input:
     tuple val(meta), path(kraken_report)
@@ -24,8 +26,10 @@ process BRACKEN_BRACKEN {
     def read_length = meta.read_length ?: 150
     def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def bracken_version = '2.6.2'
     bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    def VERSION = '2.7'
     """
     bracken \\
         ${args} \\
@@ -35,7 +39,7 @@ process BRACKEN_BRACKEN {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bracken: ${bracken_version}
+        bracken: ${VERSION}
     END_VERSIONS
     """
 }
diff --git a/tests/modules/bracken/bracken/main.nf b/tests/modules/bracken/bracken/main.nf
index f882439be96e..190aeb7051ed 100644
--- a/tests/modules/bracken/bracken/main.nf
+++ b/tests/modules/bracken/bracken/main.nf
@@ -14,8 +14,8 @@ workflow test_bracken_bracken_single_end_default_args {
 
     ch_db = UNTAR ( [[:], db] ).untar
         .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
 }
 
 workflow test_bracken_bracken_single_end_custom_args {
@@ -26,8 +26,8 @@ workflow test_bracken_bracken_single_end_custom_args {
 
     ch_db = UNTAR ( [[:], db] ).untar
         .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
 }
 
 workflow test_bracken_bracken_paired_end_default_args {
@@ -39,8 +39,8 @@ workflow test_bracken_bracken_paired_end_default_args {
 
     ch_db = UNTAR ( [[:], db] ).untar
         .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
 }
 
 workflow test_bracken_bracken_paired_end_custom_args {
@@ -52,6 +52,6 @@ workflow test_bracken_bracken_paired_end_custom_args {
 
     ch_db = UNTAR ( [[:], db] ).untar
         .map { it[1] }
-    KRAKEN2_KRAKEN2 ( input, ch_db )
-    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+    KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
 }
diff --git a/tests/modules/bracken/bracken/test.yml b/tests/modules/bracken/bracken/test.yml
index 4c87cda70ace..373314f7ea9a 100644
--- a/tests/modules/bracken/bracken/test.yml
+++ b/tests/modules/bracken/bracken/test.yml
@@ -7,7 +7,7 @@
     - path: output/bracken/test_S.tsv
       md5sum: 4a21ae14ff8a0311d55f139af5247838
     - path: output/bracken/versions.yml
-      md5sum: ab8b1550f84a99bae80f050fe718abd0
+      md5sum: e0abdac999c0d58becd8c868dd12028b
 
 - name: bracken bracken test_bracken_bracken_single_end_custom_args
   command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config
@@ -18,7 +18,7 @@
     - path: output/bracken/test_G.tsv
       md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
     - path: output/bracken/versions.yml
-      md5sum: af87e8d4c42fbcb0469ab13912b8a9bd
+      md5sum: 7d0a1629ece197a8062271d39ed8ef74
 
 - name: bracken bracken test_bracken_bracken_paired_end_default_args
   command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config
@@ -29,7 +29,7 @@
     - path: output/bracken/test_S.tsv
       md5sum: 4a21ae14ff8a0311d55f139af5247838
     - path: output/bracken/versions.yml
-      md5sum: 4602111eb25bd19a7f9d725acc5921f6
+      md5sum: 7b58898d0b9cce1ca170ac5a82d8ecf1
 
 - name: bracken bracken test_bracken_bracken_paired_end_custom_args
   command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config
@@ -40,4 +40,4 @@
     - path: output/bracken/test_G.tsv
       md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
     - path: output/bracken/versions.yml
-      md5sum: d4618b01df5ac09cc366fe2ae7c13f06
+      md5sum: 3c9160394af663ae7808c0f77fcedae8