Merge pull request #556 from broadinstitute/dp-bump-core

bump upstream docker images
broadinstitute · Sep 23, 2024 · cc8a4b7 · cc8a4b7
2 parents 4179ee0 + a241e1f
commit cc8a4b7
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Showing 13 changed files with 66 additions and 56 deletions.
diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -15,7 +15,7 @@ task assemble {
       String   sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")
 
       Int?     machine_mem_gb
-      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
     parameter_meta{
       reads_unmapped_bam: {
@@ -115,7 +115,7 @@ task select_references {
     Int?          skani_s
     Int?          skani_c
 
-    String        docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+    String        docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     Int           machine_mem_gb = 4
     Int           cpu = 2
     Int           disk_size = 100
@@ -206,7 +206,7 @@ task scaffold {
       Float?       scaffold_min_pct_contig_aligned
 
       Int?         machine_mem_gb
-      String       docker="quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String       docker="quay.io/broadinstitute/viral-assemble:2.3.6.1"
 
       # 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")
@@ -583,7 +583,7 @@ task align_reads {
     Boolean  skip_mark_dupes = false
 
     Int?     machine_mem_gb
-    String   docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String   docker = "quay.io/broadinstitute/viral-core:2.3.6"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -720,7 +720,7 @@ task refine_assembly_with_aligned_reads {
       Int      min_coverage = 3
 
       Int      machine_mem_gb = 15
-      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
 
     Int disk_size = 375
@@ -845,7 +845,7 @@ task refine_2x_and_plot {
       String? plot_coverage_novoalign_options = "-r Random -l 40 -g 40 -x 20 -t 100 -k"
 
       Int?    machine_mem_gb
-      String  docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String  docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
 
       # do this in two steps in case the input doesn't actually have "cleaned" in the name
       String  sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -981,7 +981,7 @@ task run_discordance {
       String out_basename = "run"
       Int    min_coverage = 4
 
-      String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+      String docker = "quay.io/broadinstitute/viral-core:2.3.6"
     }
     parameter_meta {
       reads_aligned_bam: {

diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl
@@ -6,7 +6,7 @@ task merge_tarballs {
     String       out_filename
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
 
   Int disk_size = 2625
@@ -163,7 +163,7 @@ task illumina_demux {
 
     Int?    machine_mem_gb
     Int     disk_size = 2625
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
 
   parameter_meta {

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:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   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:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   Int disk_size = 200
@@ -351,7 +351,7 @@ task index_ref {
     File?  novocraft_license
 
     Int?   machine_mem_gb
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
 
   Int disk_size = 100
@@ -476,7 +476,7 @@ task merge_vcfs_gatk {
     File        ref_fasta
 
     Int?        machine_mem_gb
-    String      docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String      docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     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/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
+    String    docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
   Int disk_size = 200
   command <<<
@@ -145,8 +145,13 @@ task lofreq {
     lofreq version | grep version | sed 's/.* \(.*\)/\1/g' | tee LOFREQ_VERSION
 
     # make local copies because CWD is writeable but localization dir isn't always
-    cp "~{reference_fasta}" reference.fasta
     cp "~{aligned_bam}" aligned.bam
+    python3<<CODE
+    import shutil
+    import util.file
+    with util.file.fastas_with_sanitized_ids("~{reference_fasta}", use_tmp=True) as sanitized_fastas:
+        shutil.copyfile(sanitized_fastas[0], 'reference.fasta')
+    CODE
 
     # samtools faidx fails if fasta is empty
     if [ $(grep -v '^>' reference.fasta | tr -d '\nNn' | wc -c) == "0" ]; then
@@ -191,7 +196,7 @@ task isnvs_per_sample {
     Boolean removeDoublyMappedReads = true
 
     Int?    machine_mem_gb
-    String  docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String  docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     String  sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
   }
@@ -234,7 +239,7 @@ task isnvs_vcf {
     Boolean        naiveFilter = false
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -308,7 +313,7 @@ task annotate_vcf_snpeff {
     String?        emailAddress
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     String         output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
   }

diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl
@@ -15,7 +15,7 @@ task trim_rmdup_subsamp {
         Int cpu            = 16
         Int disk_size_gb   = 100 
 
-        String docker      = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+        String docker      = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
 
     parameter_meta {

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:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   command {
@@ -38,7 +38,7 @@ task download_annotations {
     String         emailAddress
     String         combined_out_prefix
 
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   command <<<
@@ -85,7 +85,7 @@ task annot_transfer {
     File         reference_fasta
     Array[File]+ reference_feature_table
 
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -139,7 +139,7 @@ task align_and_annot_transfer_single {
     Array[File]+ reference_fastas
     Array[File]+ reference_feature_tables
 
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -192,7 +192,7 @@ task structured_comments {
 
     File?  filter_to_ids
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   String out_base = basename(assembly_stats_tsv, '.txt')
   command <<<
@@ -272,7 +272,7 @@ task rename_fasta_header {
 
     String out_basename = basename(genome_fasta, ".fasta")
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   command {
     set -e
@@ -437,7 +437,7 @@ task sra_meta_prep {
     Boolean     paired
 
     String      out_name = "sra_metadata.tsv"
-    String      docker="quay.io/broadinstitute/viral-core:2.3.2"
+    String      docker="quay.io/broadinstitute/viral-core:2.3.6"
   }
   Int disk_size = 100
   parameter_meta {
@@ -653,7 +653,7 @@ task biosample_to_genbank {
     File?   filter_to_ids
 
     Boolean s_dropout_note = true
-    String  docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String  docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
   String base = basename(biosample_attributes, ".txt")
   command {
@@ -851,7 +851,7 @@ task prepare_genbank {
     String?      assembly_method_version
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {

diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -321,7 +321,7 @@ task derived_cols {
         String?       lab_highlight_loc
         Array[File]   table_map = []
 
-        String        docker = "quay.io/broadinstitute/viral-core:2.3.2"
+        String        docker = "quay.io/broadinstitute/viral-core:2.3.6"
         Int           disk_size = 50
     }
     parameter_meta {
@@ -889,7 +889,7 @@ task filter_sequences_to_list {
 
         String       out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
         # Prior docker image: "nextstrain/base:build-20240318T173028Z"
-        String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+        String       docker = "quay.io/broadinstitute/viral-core:2.3.6"
         Int          disk_size = 750
     }
     parameter_meta {
@@ -990,7 +990,7 @@ task mafft_one_chr {
         Boolean  large = false
         Boolean  memsavetree = false
 
-        String   docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
         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:2.1.20.2"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
         Int      mem_size = 32
         Int      cpus = 64
         Int      disk_size = 750

diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl
@@ -84,7 +84,7 @@ task group_bams_by_sample {
 task get_bam_samplename {
   input {
     File    bam
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   Int   disk_size = round(size(bam, "GB")) + 50
   command <<<
@@ -111,7 +111,7 @@ task get_sample_meta {
   input {
     Array[File] samplesheets_extended
 
-    String      docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String      docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   Int disk_size = 50
   command <<<
@@ -172,7 +172,7 @@ task merge_and_reheader_bams {
       File?        reheader_table
       String       out_basename = basename(in_bams[0], ".bam")
 
-      String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+      String       docker = "quay.io/broadinstitute/viral-core:2.3.6"
       Int          disk_size = 750
       Int          machine_mem_gb = 4
     }
@@ -244,7 +244,7 @@ task rmdup_ubam {
     String  method = "mvicuna"
 
     Int     machine_mem_gb = 7
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
 
   Int disk_size = 375
@@ -303,7 +303,7 @@ task downsample_bams {
     Boolean      deduplicateAfter = false
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
 
   Int disk_size = 750
@@ -367,7 +367,7 @@ task FastqToUBAM {
     String? sequencing_center
     String? additional_picard_options
 
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   Int disk_size = 375
   parameter_meta {
@@ -418,7 +418,7 @@ task read_depths {
     File      aligned_bam
 
     String    out_basename = basename(aligned_bam, '.bam')
-    String    docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String    docker = "quay.io/broadinstitute/viral-core:2.3.6"
   }
   Int disk_size = 200
   command <<<