From 208415c5f7aa7e620004904a714af02efed724f4 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 14 Apr 2023 10:56:18 +0200
Subject: [PATCH 1/4] Bump chromap/index version

---
 modules/nf-core/chromap/index/main.nf        | 6 +++---
 tests/modules/nf-core/chromap/index/test.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf
index 0630c614d35..25ee6a7eb63 100644
--- a/modules/nf-core/chromap/index/main.nf
+++ b/modules/nf-core/chromap/index/main.nf
@@ -2,10 +2,10 @@ process CHROMAP_INDEX {
     tag "$fasta"
     label 'process_medium'
 
-    conda "bioconda::chromap=0.2.1"
+    conda "bioconda::chromap=0.2.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' :
-        'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }"
+        'https://depot.galaxyproject.org/singularity/chromap:0.2.4--hd03093a_0' :
+        'quay.io/biocontainers/chromap:0.2.4--hd03093a_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml
index d71767471d8..b5e6f74f92d 100644
--- a/tests/modules/nf-core/chromap/index/test.yml
+++ b/tests/modules/nf-core/chromap/index/test.yml
@@ -5,5 +5,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
+      md5sum: 4f30e1b5c7cb8575e24842c75d43a3dd
     - path: output/chromap/versions.yml
-      md5sum: fc5c80190d0622ea3e979e6862f8e32b

From cacf679c45de47bb13734cbfbad1a43857a92ee7 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 14 Apr 2023 10:56:40 +0200
Subject: [PATCH 2/4] Bump chromap/chromap version

---
 modules/nf-core/chromap/chromap/main.nf        | 6 +++---
 tests/modules/nf-core/chromap/chromap/test.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf
index f47995b3756..5b7631cb54c 100644
--- a/modules/nf-core/chromap/chromap/main.nf
+++ b/modules/nf-core/chromap/chromap/main.nf
@@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::chromap=0.2.1 bioconda::samtools=1.16.1"
+    conda "bioconda::chromap=0.2.4 bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/tests/modules/nf-core/chromap/chromap/test.yml b/tests/modules/nf-core/chromap/chromap/test.yml
index 6c507773387..7c1a9a0edcf 100644
--- a/tests/modules/nf-core/chromap/chromap/test.yml
+++ b/tests/modules/nf-core/chromap/chromap/test.yml
@@ -28,5 +28,5 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/test.bam
-      md5sum: 28ccaa8e39ecf5617dc270bdd7ddf1ba
+      md5sum: 7f8af20a3fa52b2a8967977f0376f466
     - path: output/chromap/versions.yml

From 310c1aa66cae757b8afb67757d47bd0ea4da10ec Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 14 Apr 2023 10:56:53 +0200
Subject: [PATCH 3/4] Update md5 hash

---
 tests/subworkflows/nf-core/fastq_align_chromap/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
index c9b49f7bb16..0e79cd7d4f7 100644
--- a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
+++ b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
@@ -51,7 +51,7 @@
     - path: ./output/samtools/test.sorted.bam.bai
       # samtools stats
     - path: ./output/samtools/test.sorted.bam.flagstat
-      md5sum: 7845b46e1dfdb6cea776bab7acf6f1e3
+      md5sum: 2fa0d90162a1b655863796c2a6bd8f45
     - path: ./output/samtools/test.sorted.bam.idxstats
       md5sum: 1adb27b52d4d64b826f48b59d61dcd4d
     - path: ./output/samtools/test.sorted.bam.stats

From b0e0de945df69ce44b550d8cd06e6cc760cec3a6 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 14 Apr 2023 11:15:36 +0200
Subject: [PATCH 4/4] Fix conda test

---
 tests/modules/nf-core/chromap/index/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml
index b5e6f74f92d..e3de1391482 100644
--- a/tests/modules/nf-core/chromap/index/test.yml
+++ b/tests/modules/nf-core/chromap/index/test.yml
@@ -5,5 +5,4 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: 4f30e1b5c7cb8575e24842c75d43a3dd
     - path: output/chromap/versions.yml