Merge pull request #639 from broadinstitute/bump-viral-ngs

viral-ngs 3.0.5 to 3.0.6

Author: dpark01

pipes/WDL/tasks/tasks_assembly.wdl

@@ -16,7 +16,7 @@ task assemble {
 
       Int?     machine_mem_gb
       Int?     cpu
-      String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+      String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
     }
     parameter_meta{
       reads_unmapped_bam: {
@@ -125,7 +125,7 @@ task select_references {
     Int?          skani_c
     Int?          skani_n
 
-    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
     Int           machine_mem_gb = 4
     Int           cpu = 2
     Int           disk_size = 100
@@ -225,7 +225,7 @@ task scaffold {
       Float?       scaffold_min_pct_contig_aligned
 
       Int?         machine_mem_gb
-      String       docker="ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+      String       docker="ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
 
       # do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
       String       sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -478,7 +478,7 @@ task skani_triangle {
     Int     compression_factor = 10
     Int     min_aligned_frac = 15
 
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
     Int     machine_mem_gb = 8
     Int     cpu = 4
     Int     disk_size = 100
@@ -721,7 +721,7 @@ task align_reads {
 
     Int?     cpu
     Int?     machine_mem_gb
-    String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -890,7 +890,7 @@ task refine_assembly_with_aligned_reads {
       Int      min_coverage = 3
 
       Int      machine_mem_gb = 8
-      String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+      String   docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
     }
 
     Int disk_size = 375
@@ -1027,7 +1027,7 @@ task run_discordance {
       String out_basename = "run"
       Int    min_coverage = 4
 
-      String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+      String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
     }
     parameter_meta {
       reads_aligned_bam: {
@@ -1276,7 +1276,7 @@ task wgsim {
         Int?   random_seed
 
         Int    machine_mem_gb = 7
-        String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-assemble"
+        String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-assemble"
     }
 
     parameter_meta {

pipes/WDL/tasks/tasks_demux.wdl

@@ -6,7 +6,7 @@ task merge_tarballs {
     String       out_filename
 
     Int?         machine_mem_gb
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   Int disk_size = 2625
@@ -182,7 +182,7 @@ task illumina_demux {
     Int?    machine_mem_gb
     # Note: GCP local SSDs must be allocated in pairs (2, 4, 8, 16, 24 × 375GB), so use 3000 (8 SSDs) instead of 2625 (7 SSDs)
     Int     disk_size = 3000
-    String  docker    = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String  docker    = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   parameter_meta {
@@ -824,7 +824,7 @@ task get_illumina_run_metadata {
     String? sequencing_center
 
     Int?   machine_mem_gb
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   parameter_meta {
@@ -928,7 +928,7 @@ task demux_fastqs {
     Int?    machine_mem_gb
     Int     max_cpu = 32       # Maximum CPU cap for autoscaling (use 16 for 2-barcode, 64 for 3-barcode)
     Int     disk_size = 750
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   # Calculate total input size for autoscaling
@@ -1057,7 +1057,7 @@ task merge_demux_metrics {
   input {
     Array[File]+ metrics_files
     String       output_filename = "merged_demux_metrics.txt"
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   parameter_meta {

pipes/WDL/tasks/tasks_interhost.wdl

@@ -160,7 +160,7 @@ task multi_align_mafft_ref {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   String         fasta_basename = basename(reference_fasta, '.fasta')
@@ -207,7 +207,7 @@ task multi_align_mafft {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   Int disk_size = 200
@@ -351,7 +351,7 @@ task index_ref {
     File?  novocraft_license
 
     Int?   machine_mem_gb
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   Int disk_size = 100
@@ -476,7 +476,7 @@ task merge_vcfs_gatk {
     File        ref_fasta
 
     Int?        machine_mem_gb
-    String      docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String      docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
 
     String      output_prefix = "merged"
   }

pipes/WDL/tasks/tasks_intrahost.wdl

@@ -136,7 +136,7 @@ task lofreq {
     File      reference_fasta
 
     String    out_basename = basename(aligned_bam, '.bam')
-    String    docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String    docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
   Int disk_size = 200
   command <<<
@@ -196,7 +196,7 @@ task isnvs_per_sample {
     Boolean removeDoublyMappedReads = true
 
     Int?    machine_mem_gb
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
 
     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 = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   parameter_meta {
@@ -313,7 +313,7 @@ task annotate_vcf_snpeff {
     String?        emailAddress
 
     Int?           machine_mem_gb
-    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
 
     String         output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
   }

pipes/WDL/tasks/tasks_megablast.wdl

@@ -15,7 +15,7 @@ task trim_rmdup_subsamp {
         Int cpu            = 16
         Int disk_size_gb   = 100 
 
-        String docker      = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+        String docker      = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
     }
 
     parameter_meta {
@@ -75,7 +75,7 @@ task lca_megablast {
         Int     cpu            = 16
         Int     disk_size_gb   = 300
 
-        String  docker         = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+        String  docker         = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
     }
     parameter_meta {
         trimmed_fasta: {

pipes/WDL/tasks/tasks_metagenomics.wdl

@@ -218,7 +218,7 @@ task kraken2 {
     Int?   min_base_qual
 
     Int    machine_mem_gb = 90
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   parameter_meta {
@@ -351,7 +351,7 @@ task report_primary_kraken_taxa {
     File          kraken_summary_report
     String        focal_taxon = "Viruses"
 
-    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
   String out_basename = basename(kraken_summary_report, '.txt')
   Int disk_size = 50
@@ -402,7 +402,7 @@ task filter_refs_to_found_taxa {
     File          taxdump_tgz
     Int           min_read_count = 100
 
-    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
   String ref_basename = basename(taxid_to_ref_accessions_tsv, '.tsv')
   String hits_basename = basename(focal_report_tsv, '.tsv')
@@ -453,7 +453,7 @@ task build_kraken2_db {
     Int?          zstd_compression_level
 
     Int           machine_mem_gb = 100
-    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String        docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   Int disk_size = 750
@@ -595,7 +595,7 @@ task blastx {
     File   krona_taxonomy_db_tgz
 
     Int    machine_mem_gb = 8
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   parameter_meta {
@@ -685,7 +685,7 @@ task krona {
     Int?         magnitude_column
 
     Int          machine_mem_gb = 3
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   Int disk_size = 50
@@ -792,7 +792,7 @@ task filter_bam_to_taxa {
     String         out_filename_suffix = "filtered"
 
     Int            machine_mem_gb = 8
-    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix
@@ -885,7 +885,7 @@ task kaiju {
     File   krona_taxonomy_db_tgz  # taxonomy/taxonomy.tab
 
     Int    machine_mem_gb = 100
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   String   input_basename = basename(reads_unmapped_bam, ".bam")

pipes/WDL/tasks/tasks_ncbi.wdl

@@ -6,7 +6,7 @@ task download_fasta {
     Array[String]+ accessions
     String         emailAddress
 
-    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   command <<<
@@ -42,7 +42,7 @@ task download_fasta_from_accession_string {
     String out_prefix
     String emailAddress
 
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   command <<<
@@ -94,7 +94,7 @@ task download_annotations {
     String         emailAddress
     String         combined_out_prefix
 
-    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String         docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   command <<<
@@ -136,7 +136,7 @@ task download_ref_genomes_from_tsv {
     File      ref_genomes_tsv    # [tax_id, isolate_prefix, taxname, colon_delim_accession_list]
     String    emailAddress
 
-    String    docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String    docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   command <<<
@@ -183,7 +183,7 @@ task sequencing_platform_from_bam {
   input {
     File    bam
 
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
 
   command <<<
@@ -238,7 +238,7 @@ task align_and_annot_transfer_single {
 
     String       out_basename = basename(genome_fasta, '.fasta')
     Int          machine_mem_gb = 30
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"
   }
 
   parameter_meta {
@@ -293,7 +293,7 @@ task structured_comments {
 
     File?  filter_to_ids
 
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
   String out_base = basename(assembly_stats_tsv, '.txt')
   command <<<
@@ -346,7 +346,7 @@ task structured_comments_from_aligned_bam {
     String  out_basename = basename(aligned_bam, '.bam')
     Boolean is_genome_assembly = true
     Boolean sanitize_ids = true
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
   # see https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/
   command <<<
@@ -465,7 +465,7 @@ task rename_fasta_header {
 
     String out_basename = basename(genome_fasta, ".fasta")
 
-    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
   command <<<
     set -e
@@ -630,7 +630,7 @@ task sra_meta_prep {
     Boolean     paired
 
     String      out_name = "sra_metadata.tsv"
-    String      docker="ghcr.io/broadinstitute/viral-ngs:3.0.5-core"
+    String      docker="ghcr.io/broadinstitute/viral-ngs:3.0.6-core"
   }
   Int disk_size = 100
   parameter_meta {
@@ -1246,7 +1246,7 @@ task table2asn {
 
     String       out_basename = basename(assembly_fasta, ".fasta")
     Int          machine_mem_gb = 8
-    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-phylo"  # this could be a simpler docker image, we don't use anything beyond table2asn itself
+    String       docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-phylo"  # this could be a simpler docker image, we don't use anything beyond table2asn itself
   }
   Int disk_size = 50
 
@@ -1338,7 +1338,7 @@ task package_special_genbank_ftp_submission {
     String account_name
     String wizard="BankIt_SARSCoV2_api"
 
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-baseimage"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-baseimage"
   }
   command <<<
     set -e
@@ -1403,7 +1403,7 @@ task genbank_special_taxa {
     Int     taxid
     File    taxdump_tgz
     File    vadr_by_taxid_tsv # "gs://pathogen-public-dbs/viral-references/annotation/vadr/vadr-by-taxid.tsv"
-    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.5-classify"
+    String  docker = "ghcr.io/broadinstitute/viral-ngs:3.0.6-classify"
   }
 
   command <<<