Bump bwa-mem2 container build and update Conda env

- update Conda environments to use fixed Sambamba Bioconda package - new container build also uses fixed Sambamba package
nf-core · May 27, 2024 · 610ea8a · 610ea8a
1 parent b0cf4ce
commit 610ea8a
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/modules/local/bwa-mem2/mem/environment.yml b/modules/local/bwa-mem2/mem/environment.yml
@@ -6,4 +6,4 @@ channels:
 dependencies:
   - bioconda::bwa-mem2=2.2.1
   - bioconda::samtools=1.19.2
-  - bioconda::sambamba=1.0
+  - bioconda::sambamba=1.0.1
diff --git a/modules/local/bwa-mem2/mem/main.nf b/modules/local/bwa-mem2/mem/main.nf
@@ -4,8 +4,8 @@ process BWAMEM2_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' :
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' }"
 
     input:
     tuple val(meta), path(reads_fwd), path(reads_rev)

diff --git a/modules/local/custom/lilac_extract_and_index_contig/main.nf b/modules/local/custom/lilac_extract_and_index_contig/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_EXTRACTCONTIG {
 
     conda "bwa-mem2=2.2.1 samtools=1.19.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' :
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' }"
 
     input:
     val contig_name

diff --git a/modules/local/custom/lilac_realign_reads_lilac/main.nf b/modules/local/custom/lilac_realign_reads_lilac/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_REALIGNREADS {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.19.2 bioconda::sambamba=1.0"
+    conda "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.19.2 bioconda::sambamba=1.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' :
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:4163e62e1daead7b7ea0228baece715bec295c22-0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)