Merge pull request #5 from Kincekara/1.4.0-dev

1.4.0
Kincekara · Jan 26, 2024 · 916f3e3 · 916f3e3
2 parents e2154df + 9d2e28d
commit 916f3e3
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Showing 9 changed files with 15 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -35,16 +35,16 @@ The following programs and tools are used in the C-BIRD pipeline.
 | Tools | Version | Comments |
 | --- | --- | --- |
 | [FastP](https://github.com/OpenGene/fastp) | 0.23.4 | QC, adapter removal, quality filtering and trimming |
-| [BBTools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/) | 39.01 | phiX removal & optional normalization |
+| [BBTools](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/) | 39.06 | phiX removal & optional normalization |
 | [Kraken2](https://github.com/DerrickWood/kraken2) | 2.1.3 | Taxonomic profiling & contamination check |
 | [Bracken](https://github.com/jenniferlu717/Bracken) | 2.9 | Abundance estimation |
 | [SPAdes](https://github.com/ablab/spades) | 3.15.5 | *De novo* assembly |
 | [Mash](https://github.com/marbl/Mash) | 2.3 | Bacterial identification |
 | [QUAST](https://github.com/ablab/quast) | 5.2.0 | Genome assembly evaluation |
-| [BUSCO](https://gitlab.com/ezlab/busco/-/tree/master) | 5.4.7 | Genomic data quality assesment |
-| [mlst](https://github.com/tseemann/mlst) | 2.22.0 | MLST typing |
-| [AMRFinderPlus](https://github.com/ncbi/amr) | 3.11.20 | AMR gene identification |
-| [BLAST+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html)| 2.14.0 | Target gene search |
+| [BUSCO](https://gitlab.com/ezlab/busco/-/tree/master) | 5.6.1 | Genomic data quality assesment |
+| [mlst](https://github.com/tseemann/mlst) | 2.23.0 | MLST typing |
+| [AMRFinderPlus](https://github.com/ncbi/amr) | 3.11.26 | AMR gene identification |
+| [BLAST+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html)| 2.15.0 | Target gene search |
 | [PlasmidFinder](https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/) | 2.1.6 | Plasmid detection |
 | Cbird-Util | 1.0 | Individual summary report generation |
 

diff --git a/tasks/task_amrfinderplus.wdl b/tasks/task_amrfinderplus.wdl
@@ -9,7 +9,7 @@ task amrfinderplus_nuc {
     Float? minid
     Float? mincov
     Int cpu = 4
-    String docker = "staphb/ncbi-amrfinderplus:3.11.20-2023-09-26.1"
+    String docker = "staphb/ncbi-amrfinderplus:3.11.26-2023-11-15.1"
   }
   command <<<
     # logging info
@@ -93,6 +93,8 @@ task amrfinderplus_nuc {
       "Streptococcus agalactiae"
       "Streptococcus pyogenes"
       "Vibrio cholerae"
+      "Vibrio parahaemolyticus"
+      "Vibrio vulnificus"
     )
 
     # check organism in curated organism list

diff --git a/tasks/task_bbtools.wdl b/tasks/task_bbtools.wdl
@@ -11,7 +11,7 @@ task assembly_prep {
     Int min_depth = 5
     Int read_threshold = 8000000
     Int memory = 8
-    String docker = "kincekara/bbtools:39.03"
+    String docker = "kincekara/bbtools:39.06"
   }
 
   command <<<

diff --git a/tasks/task_blast.wdl b/tasks/task_blast.wdl
@@ -8,7 +8,7 @@ task tblastn {
     Float evalue = 0.001
     Int max_hsps = 1
     Int percent_identity = 90
-    String docker = "staphb/blast:2.14.0"
+    String docker = "staphb/blast:2.15.0"
   }
 
   command <<<

diff --git a/tasks/task_busco.wdl b/tasks/task_busco.wdl
@@ -4,7 +4,7 @@ task busco {
   input {
     File assembly   
     String samplename
-    String docker = "kincekara/busco:5.4.7-bacteria_odb10.2020-03-06"
+    String docker = "staphb/busco:5.6.1-prok-bacteria_odb10_2024-01-08"
     Int? memory = 16
     Int? cpu = 4
   }

diff --git a/tasks/task_mlst.wdl b/tasks/task_mlst.wdl
@@ -7,7 +7,7 @@ task ts_mlst {
   input {
     File assembly
     String samplename
-    String docker = "staphb/mlst:2.23.0-2023-08"
+    String docker = "staphb/mlst:2.23.0-2024-01"
     Int? cpu = 4
     # Parameters
     # --nopath          Strip filename paths from FILE column (default OFF)

diff --git a/tasks/task_ncbi_datasets.wdl b/tasks/task_ncbi_datasets.wdl
@@ -4,7 +4,7 @@ task fetch_reference {
   input {
     String samplename
     String taxon
-    String docker = "kincekara/cbird-util:alpine-v0.8"
+    String docker = "kincekara/cbird-util:alpine-v1.0"
   }
 
   command <<<    

diff --git a/tasks/task_taxonomy.wdl b/tasks/task_taxonomy.wdl
@@ -12,7 +12,7 @@ task profile {
     String? min_hit_groups = 3
     Int? memory = 32
     Int? cpu = 4
-    String? kraken2_db_version = "Standard-8 2023-06-05"
+    String? kraken2_db_version = "Standard-8 2023-10-09"
   }
 
   command <<<

diff --git a/tasks/task_version.wdl b/tasks/task_version.wdl
@@ -8,7 +8,7 @@ task version_capture {
     volatile: true
   }
   command {
-    cbird_version="C-BIRD v1.3.0"
+    cbird_version="C-BIRD v1.4.0"
     ~{default='' 'export TZ=' + timezone}
     date +"%Y-%m-%d" > TODAY
     echo "$cbird_version" > CBIRD_VERSION