bump pinned docker versions; temporarily skip enforcement of version …

…pinning for viral-classify in tasks_megablast.wdl
broadinstitute · Jun 19, 2024 · 6e6f2f6 · 6e6f2f6
1 parent c44f1fd
commit 6e6f2f6
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Showing 5 changed files with 16 additions and 15 deletions.
diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl
@@ -12,7 +12,7 @@ task trim_rmdup_subsamp {
         Int machine_mem_gb = 128
         Int cpu = 16
         Int disk_size_gb = 100 
-        String docker ="quay.io/broadinstitute/viral-assemble:2.3.1.3"
+        String docker ="quay.io/broadinstitute/viral-assemble:2.3.1.4"
     }
     parameter_meta {
         inBam: {
@@ -168,6 +168,7 @@ task ChunkBlastHits {
         Int    cpu = 16
         Int    disk_size_gb = 300
         String docker = "quay.io/broadinstitute/viral-classify:fn_blast"
+        String docker = "quay.io/broadinstitute/viral-classify:fn_blast" #skip-global-version-pin
     }
         String fasta_basename = basename(inFasta, ".fasta")
         #setting current working directory as logging outputs
@@ -247,7 +248,7 @@ task blastoff {
         Int     machine_mem_gb = 64 
         Int     cpu = 16
         Int     disk_size_gb = 300
-        String  docker = "quay.io/broadinstitute/viral-classify:fn_blast"
+        String  docker = "quay.io/broadinstitute/viral-classify:fn_blast" #skip-global-version-pin
 
     }
         #setting current working directory as logging outputs

diff --git a/pipes/WDL/tasks/tasks_metagenomics.wdl b/pipes/WDL/tasks/tasks_metagenomics.wdl
@@ -213,7 +213,7 @@ task kraken2 {
     Int?   min_base_qual
 
     Int    machine_mem_gb = 90
-    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   parameter_meta {
@@ -335,7 +335,7 @@ task report_primary_kraken_taxa {
     File          kraken_summary_report
     String        focal_taxon = "Viruses"
 
-    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
   String out_basename = basename(kraken_summary_report, '.txt')
   Int disk_size = 50
@@ -386,7 +386,7 @@ task filter_refs_to_found_taxa {
     File          taxdump_tgz
     Int           min_read_count = 100
 
-    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
   String ref_basename = basename(taxid_to_ref_accessions_tsv, '.tsv')
   String hits_basename = basename(focal_report_tsv, '.tsv')
@@ -437,7 +437,7 @@ task build_kraken2_db {
     Int?          zstd_compression_level
 
     Int           machine_mem_gb = 100
-    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String        docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   Int disk_size = 750
@@ -579,7 +579,7 @@ task blastx {
     File   krona_taxonomy_db_tgz
 
     Int    machine_mem_gb = 8
-    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   parameter_meta {
@@ -669,7 +669,7 @@ task krona {
     Int?         magnitude_column
 
     Int          machine_mem_gb = 3
-    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   Int disk_size = 50
@@ -776,7 +776,7 @@ task filter_bam_to_taxa {
     String         out_filename_suffix = "filtered"
 
     Int            machine_mem_gb = 26
-    String         docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String         docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix
@@ -863,7 +863,7 @@ task kaiju {
     File   krona_taxonomy_db_tgz  # taxonomy/taxonomy.tab
 
     Int    machine_mem_gb = 100
-    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   String   input_basename = basename(reads_unmapped_bam, ".bam")

diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
@@ -538,7 +538,7 @@ task aggregate_metagenomics_reports {
     String       aggregate_taxlevel_focus                 = "species"
     Int          aggregate_top_N_hits                     = 5
 
-    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   parameter_meta {

diff --git a/pipes/WDL/tasks/tasks_taxon_filter.wdl b/pipes/WDL/tasks/tasks_taxon_filter.wdl
@@ -14,7 +14,7 @@ task deplete_taxa {
 
     Int          cpu = 8
     Int          machine_mem_gb = 15
-    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String       docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   parameter_meta {
@@ -113,7 +113,7 @@ task filter_to_taxon {
     String   neg_control_prefixes_space_separated = "neg water NTC"
 
     Int      machine_mem_gb = 15
-    String   docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String   docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   # do this in two steps in case the input doesn't actually have "cleaned" in the name
@@ -172,7 +172,7 @@ task build_lastal_db {
     File   sequences_fasta
 
     Int    machine_mem_gb = 7
-    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.0"
+    String docker = "quay.io/broadinstitute/viral-classify:2.2.4.2"
   }
 
   String db_name = basename(sequences_fasta, ".fasta")

diff --git a/requirements-modules.txt b/requirements-modules.txt
@@ -1,6 +1,6 @@
 broadinstitute/viral-core=2.3.1
 broadinstitute/viral-assemble=2.3.1.4
-broadinstitute/viral-classify=2.2.4.0
+broadinstitute/viral-classify=2.2.4.2
 broadinstitute/viral-phylo=2.1.20.2
 broadinstitute/py3-bio=0.1.2
 broadinstitute/beast-beagle-cuda=1.10.5pre