From 62da45b0e1202677a07e2da0ee9f6181466232fb Mon Sep 17 00:00:00 2001
From: Jose Espinosa-Carrasco <kadomu@gmail.com>
Date: Thu, 10 Mar 2022 09:23:45 +0100
Subject: [PATCH] Bump chromap version 0.2.0 (#1374)

* Bump chromap version 0.2.0

* Temporary use the docker container until singularity container becomes available

* Temporary use the docker container until singularity container available

* Remove empty lines

* Update singularity container after became available
---
 modules/chromap/chromap/main.nf        | 6 +++---
 modules/chromap/index/main.nf          | 7 +++----
 tests/modules/chromap/chromap/test.yml | 8 +++++++-
 tests/modules/chromap/index/test.yml   | 2 ++
 4 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf
index cdbf6049..4ee86b92 100644
--- a/modules/chromap/chromap/main.nf
+++ b/modules/chromap/chromap/main.nf
@@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.0 bioconda::samtools=1.14" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf
index 52deaf06..2696d6a5 100644
--- a/modules/chromap/index/main.nf
+++ b/modules/chromap/index/main.nf
@@ -2,11 +2,10 @@ process CHROMAP_INDEX {
     tag '$fasta'
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
-        'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }"
-
+        'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' :
+        'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }"
 
     input:
     path fasta
diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml
index 09e5e753..40e45959 100644
--- a/tests/modules/chromap/chromap/test.yml
+++ b/tests/modules/chromap/chromap/test.yml
@@ -7,6 +7,8 @@
     - path: output/chromap/genome.index
     - path: output/chromap/test.bed.gz
       md5sum: 25e40bde24c7b447292cd68573728694
+    - path: output/chromap/versions.yml
+      md5sum: 2d3d2959ac20d98036807964896829e7
 
 - name: chromap chromap test_chromap_chromap_paired_end
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -17,6 +19,8 @@
     - path: output/chromap/genome.index
     - path: output/chromap/test.bed.gz
       md5sum: 7cdc8448882b75811e0c784f5f20aef2
+    - path: output/chromap/versions.yml
+      md5sum: 51cff66779161d8a602cce5989017395
 
 - name: chromap chromap test_chromap_chromap_paired_bam
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -26,4 +30,6 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/test.bam
-      md5sum: 73e2c76007e3c61df625668e01b3f42f
+      md5sum: f255c7441d5a1f307fc642d2aa19647e
+    - path: output/chromap/versions.yml
+      md5sum: f91910c44169549c3923931de5c3afcb
diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml
index dde1aa1b..b2aa37d8 100644
--- a/tests/modules/chromap/index/test.yml
+++ b/tests/modules/chromap/index/test.yml
@@ -5,3 +5,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
+    - path: output/chromap/versions.yml
+      md5sum: b75dec647f9dc5f4887f36d1db7a9ccd