Update software to latest versions

peterk87 · May 30, 2024 · 300eaf2 · 300eaf2
1 parent db8f3e7
commit 300eaf2
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Showing 9 changed files with 25 additions and 28 deletions.
diff --git a/modules/local/bcftools.nf b/modules/local/bcftools.nf
@@ -5,11 +5,11 @@ process BCF_CONSENSUS {
   tag "$sample|$segment|$ref_id"
   label 'process_medium'
 
-  conda 'bioconda::bcftools=1.15.1 conda-forge::gsl=2.7'
+  conda 'bioconda::bcftools=1.20 conda-forge::gsl=2.7'
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0'
+    container 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0'
   } else {
-    container 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0'
+    container 'quay.io/biocontainers/bcftools:1.20--h8b25389_0'
   }
 
   input:

diff --git a/modules/local/blast_makeblastdb.nf b/modules/local/blast_makeblastdb.nf
@@ -3,11 +3,11 @@ process BLAST_MAKEBLASTDB {
   tag "$fasta"
   label 'process_low'
 
-  conda 'bioconda::blast=2.14.0'
+  conda 'bioconda::blast=2.15.0'
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
+    container 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1'
   } else {
-    container 'quay.io/biocontainers/blast:2.14.0--h7d5a4b4_1'
+    container 'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1'
   }
 
   input:

diff --git a/modules/local/blastn.nf b/modules/local/blastn.nf
@@ -2,11 +2,11 @@ process BLAST_BLASTN {
   tag "$meta.id"
   label 'process_high'
 
-  conda 'bioconda::blast=2.14.0'
+  conda 'bioconda::blast=2.15.0'
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
+    container 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1'
   } else {
-    container 'quay.io/biocontainers/blast:2.14.0--h7d5a4b4_1'
+    container 'quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_1'
   }
 
   input:

diff --git a/modules/local/clair3.nf b/modules/local/clair3.nf
@@ -5,12 +5,12 @@ process CLAIR3 {
   tag "$sample|$segment|$ref_id"
   label 'process_low'
 
-  conda 'bioconda::clair3==1.0.5'
+  conda 'bioconda::clair3==1.0.9'
   // use official images to avoid issues with full alignment failing. See issues:
   // https://github.com/HKU-BAL/Clair3/issues/98
   // https://github.com/HKU-BAL/Clair3/issues/181
   // Biocontainers image fails for some reason.
-  container 'hkubal/clair3:v1.0.5'
+  container 'hkubal/clair3:v1.0.9'
 
   input:
   tuple val(sample), val(segment), val(ref_id), path(ref_fasta), path(bam)

diff --git a/modules/local/minimap2.nf b/modules/local/minimap2.nf
@@ -4,11 +4,11 @@ process MINIMAP2 {
   tag "$sample|$segment|$ref_id"
   label 'process_low'
 
-  conda 'bioconda::minimap2=2.24 bioconda::samtools=1.15'
+  conda 'bioconda::minimap2=2.28 bioconda::samtools=1.20'
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
+    container 'https://depot.galaxyproject.org/singularity/minimap2:2.28--he4a0461_1'
   } else {
-    container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
+    container 'quay.io/biocontainers/minimap2:2.28--he4a0461_1'
   }
 
 

diff --git a/modules/local/mosdepth.nf b/modules/local/mosdepth.nf
@@ -4,12 +4,13 @@ process MOSDEPTH_GENOME {
   tag "$sample|$segment|$ref_id"
   label 'process_low'
 
-  conda 'bioconda::mosdepth=0.3.3'
+  conda 'bioconda::mosdepth=0.3.8'
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-      container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--h37c5b7d_2"
+    container 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0'
   } else {
-      container "quay.io/biocontainers/mosdepth:0.3.3--h01d7912_0"
+    container 'quay.io/biocontainers/mosdepth:0.3.8--hd299d5a_0'
   }
+
   input:
   tuple val(sample), val(segment), val(ref_id), path(fasta), path(bam_bai)
 

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,11 +1,11 @@
 process MULTIQC {
   label 'process_low'
 
-  conda "bioconda::multiqc=1.12"
+  conda "bioconda::multiqc=1.21"
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0'
+    container 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0'
   } else {
-    container 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0'
+    container 'quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0'
   }
 
   input:

diff --git a/modules/local/seqtk_seq.nf b/modules/local/seqtk_seq.nf
@@ -5,11 +5,11 @@ process SEQTK_SEQ{
   tag "$sample|$segment|$ref_id"
   // use default process resources
 
-  conda "bioconda::seqtk=1.3"
+  conda "bioconda::seqtk=1.4"
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3'
+    container 'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2'
   } else {
-    container 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3'
+    container 'quay.io/biocontainers/seqtk:1.4--he4a0461_2'
   }
 
   input:

diff --git a/modules/local/zstd_decompress.nf b/modules/local/zstd_decompress.nf
@@ -2,11 +2,7 @@ process ZSTD_DECOMPRESS {
 
   conda 'conda-forge::zstd=1.5.2'
   // TODO: using clair3 container here for zstd and since it might be used if running the Nanopore workflow, but should move to multi-package-container with just zstd and maybe curl to combine data fetch functionality
-  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/clair3:1.0.3--py39h8492097_0'
-  } else {
-    container 'quay.io/biocontainers/clair3:1.0.3--py39h8492097_0'
-  }
+  container 'hkubal/clair3:v1.0.9'
 
   input:
   path(zstd_file, stageAs: "input*/*")