bump viral-phylo

broadinstitute · Jan 23, 2025 · fa7d0a8 · fa7d0a8
1 parent e77cf7b
commit fa7d0a8
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Showing 5 changed files with 14 additions and 14 deletions.
diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl
@@ -160,7 +160,7 @@ task multi_align_mafft_ref {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   String         fasta_basename = basename(reference_fasta, '.fasta')
@@ -207,7 +207,7 @@ task multi_align_mafft {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   Int disk_size = 200
@@ -476,7 +476,7 @@ task merge_vcfs_gatk {
     File        ref_fasta
 
     Int?        machine_mem_gb
-    String      docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String      docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
 
     String      output_prefix = "merged"
   }

diff --git a/pipes/WDL/tasks/tasks_intrahost.wdl b/pipes/WDL/tasks/tasks_intrahost.wdl
@@ -136,7 +136,7 @@ task lofreq {
     File      reference_fasta
 
     String    out_basename = basename(aligned_bam, '.bam')
-    String    docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String    docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
   Int disk_size = 200
   command <<<
@@ -196,7 +196,7 @@ task isnvs_per_sample {
     Boolean removeDoublyMappedReads = true
 
     Int?    machine_mem_gb
-    String  docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String  docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
 
     String  sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
   }
@@ -239,7 +239,7 @@ task isnvs_vcf {
     Boolean        naiveFilter = false
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   parameter_meta {
@@ -313,7 +313,7 @@ task annotate_vcf_snpeff {
     String?        emailAddress
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
 
     String         output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
   }

diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -6,7 +6,7 @@ task download_fasta {
     Array[String]+ accessions
     String         emailAddress
 
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   command {
@@ -38,7 +38,7 @@ task download_annotations {
     String         emailAddress
     String         combined_out_prefix
 
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   command <<<
@@ -132,7 +132,7 @@ task align_and_annot_transfer_single {
     Array[File]+ reference_fastas
     Array[File]+ reference_feature_tables
 
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
   String out_base = basename(genome_fasta, '.fasta')
 
@@ -1068,7 +1068,7 @@ task table2asn {
     Int          genetic_code = 1
 
     Int          machine_mem_gb = 3
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
   }
 
   String out_basename = basename(assembly_fasta, ".fasta")

diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -990,7 +990,7 @@ task mafft_one_chr {
         Boolean  large = false
         Boolean  memsavetree = false
 
-        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
         Int      mem_size = 500
         Int      cpus = 64
         Int      disk_size = 750
@@ -1078,7 +1078,7 @@ task mafft_one_chr_chunked {
         Int      batch_chunk_size = 2000
         Int      threads_per_job = 2
 
-        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.4.1.0"
         Int      mem_size = 32
         Int      cpus = 64
         Int      disk_size = 750

diff --git a/requirements-modules.txt b/requirements-modules.txt
@@ -1,7 +1,7 @@
 broadinstitute/viral-core=2.4.1
 broadinstitute/viral-assemble=2.3.6.1
 broadinstitute/viral-classify=2.2.5
-broadinstitute/viral-phylo=2.3.6.0
+broadinstitute/viral-phylo=2.4.1.0
 broadinstitute/py3-bio=0.1.2
 broadinstitute/beast-beagle-cuda=1.10.5pre
 broadinstitute/ncbi-tools=2.10.7.10