Merge pull request #112 from CDCgov/v2.0.1

v2.0.1

CHANGELOG.md

@@ -132,4 +132,17 @@ Below are the list of changes to phx since is initial release. As fixes can take
 - AMRFinder+ was updated from 3.10.45 to [3.11.11](https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.11).  
 - BUSCO was updated from 5.4.3 to [5.4.7](https://gitlab.com/ezlab/busco/-/blob/master/CHANGELOG).  
 - MultiQC was updated from 1.11 to [1.14](https://github.com/ewels/MultiQC/releases/tag/v1.14).  
-- MLST was updated from 2.22.1 to [2.23.0](https://github.com/tseemann/mlst/releases/tag/v2.23.0).  
+- MLST was updated from 2.22.1 to [2.23.0](https://github.com/tseemann/mlst/releases/tag/v2.23.0).
+
+
+## [v2.0.1](https://github.com/CDCgov/phoenix/releases/tag/v2.0.1) (07/14/2023)
+
+[Full Changelog](https://github.com/CDCgov/phoenix/compare/v2.0.0...v2.0.1)
+
+**Implemented Enhancements:**  
+- Updated nextflow towwer scheme that describes inputs.
+
+**Fixed Bugs:**  
+- Typo fix and changed branch called in Terra task that caused Terra version to crash.
+
+

modules/local/format_ANI_best_hit.nf

@@ -22,7 +22,7 @@ process FORMAT_ANI {
     }
     def container = task.container.toString() - "quay.io/jvhagey/phoenix:"
     """
-    db_version=\$(echo ${ani_file} | sed 's/.ani.sorted.txt//' | sed 's/${meta.id}_//' )
+    db_version=\$(echo ${ani_file} | sed 's/.ani.txt//' | sed 's/${meta.id}_//' )
     # Setup to catch any issues while grabbing date from DB name
     if [[ "\${db_version}" = "" ]]; then
         db_version="REFSEQ_unknown"
@@ -35,4 +35,4 @@ process FORMAT_ANI {
         phoenix_base_container: ${container}
     END_VERSIONS
     """
-}
+}

nextflow.config

@@ -188,7 +188,7 @@ manifest {
     description     = 'PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '2.0.0'
+    version         = '2.0.1'
 }
 
 // Load modules.config for DSL2 module specific options

nextflow_nftower_schema.json

@@ -88,11 +88,17 @@
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
                 },
+                "coverage": {
+                    "type": "string",
+                    "description": "If you want to increase the coverage cut off >30x use --coverage (ex. --coverage 40)",
+                    "default": "30",
+                    "fa_icon": "fas fa-hashtag"
+                },
                 "busco_db_path": {
                     "type": "string",
                     "fa_icon": "fas fa-keyboard",
-                    "description": "Path (full or relative) for where BUSCO files are if you want to run in offline mode. Use only with -entry CDC_PHOENIX",
-                    "default": "Not to run in offline mode."
+                    "description": "Path (full or relative) for where BUSCO files are if you want to run in offline mode. The database is ~250GB if you download it from https://busco-data.ezlab.org/v5/data/lineages/ . Use only with -entry CDC_PHOENIX, CDC_SCAFFOLDS or CDC_SRA.",
+                    "default": ""
                 },
                 "publish_dir_mode": {
                     "type": "string",
@@ -275,4 +281,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}

nextflow_schema.json

@@ -45,7 +45,7 @@
                 "scaffold_ext": {
                     "type": "string",
                     "fa_icon": "fas fa-keyboard",
-                    "description": "String that is the FULL extention of the scaffolds files you wish to input. For example, use if your file names are `<sample_id>.fa.gz` use `--scaffolds_ext '.fa.gz'` and if you want to look through subdirectories for files with the name `<sample_id>.fa.gz` then use `--scaffolds_ext '/*.fa.gz'` A regrex of this extension (ex. *.scaffolds.fa.gz) will then be used as default. Assemblies must end in '.fa.gz' or '.fasta.gz'.",
+                    "description": "String that is the FULL extension of the scaffolds files you wish to input. For example, use if your file names are `<sample_id>.fa.gz` use `--scaffolds_ext '.fa.gz'` and if you want to look through subdirectories for files with the name `<sample_id>.fa.gz` then use `--scaffolds_ext '/*.fa.gz'` A regrex of this extension (ex. *.scaffolds.fa.gz) will then be used as default. Assemblies must end in '.fa.gz' or '.fasta.gz'.",
                     "default": ".scaffolds.fa.gz"
                 }
             }
@@ -287,4 +287,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}

tasks/task_phoenix.wdl

@@ -58,7 +58,7 @@ task phoenix {
       scaffold_ext=""
     fi
 
-    if nextflow run cdcgov/phoenix -plugins [email protected] -profile terra -r v1.2.0-dev -entry ~{entry} --terra true $input_file --kraken2db ~{kraken2db} --coverage ~{coverage} --tmpdir $TMPDIR --max_cpus ~{cpu} --max_memory '~{memory}.GB' $scaffold_ext; then
+    if nextflow run cdcgov/phoenix -plugins [email protected] -profile terra -r v2.0.1 -entry ~{entry} --terra true $input_file --kraken2db ~{kraken2db} --coverage ~{coverage} --tmpdir $TMPDIR --max_cpus ~{cpu} --max_memory '~{memory}.GB' $scaffold_ext; then
       # Everything finished, pack up the results and clean up
       #tar -cf - work/ | gzip -n --best > work.tar.gz
       rm -rf .nextflow/ work/