From c29b3fe11a8b619925d7c90c8c6daa55ee6d38f1 Mon Sep 17 00:00:00 2001
From: WackerO <43847497+WackerO@users.noreply.github.com>
Date: Thu, 14 Jul 2022 13:51:34 +0200
Subject: [PATCH] Updated container versions for fgbio (#1878)

* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads

* Corrected fgbio call container, trying to fix fgbio group tests

* Removed incorrect line
---
 modules/fgbio/callmolecularconsensusreads/main.nf        | 6 +++---
 modules/fgbio/groupreadsbyumi/main.nf                    | 6 +++---
 tests/modules/fgbio/callmolecularconsensusreads/test.yml | 2 +-
 tests/modules/fgbio/groupreadsbyumi/test.yml             | 4 ++--
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf
index 347dc269..fc9b1b1b 100644
--- a/modules/fgbio/callmolecularconsensusreads/main.nf
+++ b/modules/fgbio/callmolecularconsensusreads/main.nf
@@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null)
+    conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' :
-        'quay.io/biocontainers/fgbio:1.3.0--0' }"
+        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
+        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/fgbio/groupreadsbyumi/main.nf b/modules/fgbio/groupreadsbyumi/main.nf
index 31250d23..7c09ab7c 100644
--- a/modules/fgbio/groupreadsbyumi/main.nf
+++ b/modules/fgbio/groupreadsbyumi/main.nf
@@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null)
+    conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
+        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(taggedbam)
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/test.yml b/tests/modules/fgbio/callmolecularconsensusreads/test.yml
index 5e26cd01..61ddb382 100644
--- a/tests/modules/fgbio/callmolecularconsensusreads/test.yml
+++ b/tests/modules/fgbio/callmolecularconsensusreads/test.yml
@@ -5,6 +5,6 @@
     - fgbio/callmolecularconsensusreads
   files:
     - path: output/fgbio/test_molreads.bam
-      md5sum: 7010bcdc037c36af13dbc370c06c76d3
+      md5sum: 6ae57429e3218f5eba9555d597b7c60f
     - path: output/fgbio/test_out.bam
       md5sum: d84e28fecc90c0752c543e934f10aa31
diff --git a/tests/modules/fgbio/groupreadsbyumi/test.yml b/tests/modules/fgbio/groupreadsbyumi/test.yml
index c1cfd4f0..529a07e5 100644
--- a/tests/modules/fgbio/groupreadsbyumi/test.yml
+++ b/tests/modules/fgbio/groupreadsbyumi/test.yml
@@ -5,6 +5,6 @@
     - fgbio/groupreadsbyumi
   files:
     - path: output/fgbio/test_umi-grouped.bam
-      md5sum: f1e53fc845fd99a3da172eb8063dff0b
+      md5sum: c7a9aee0b9b277c85d6a112d3021082d
     - path: output/fgbio/test_umi_histogram.txt
-      md5sum: d17fd167b2a765d46e4b01bf08ece01b
+      md5sum: f2f29523bb7016e1a78fe634466cbfba