Merge branch 'main' into dependabot/submodules/pipeline-submodules-51…

…de11d00e
uclahs-cds · Sep 12, 2024 · 176bed2 · 176bed2
2 parents 6dbb4d6 + bd98eb4
commit 176bed2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,7 +7,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
-## [Unreleased]
+## [1.0.0] - 2024-09-10
 
 ### Added
 

diff --git a/README.md b/README.md
diff --git a/config/F16.config b/config/F16.config
diff --git a/config/F2.config b/config/F2.config
diff --git a/config/F32.config b/config/F32.config
diff --git a/config/F72.config b/config/F72.config
diff --git a/config/M64.config b/config/M64.config
diff --git a/config/default.config b/config/default.config
@@ -22,7 +22,7 @@ params {
     gatk_version       = '4.4.0.0'
     pipeval_version    = '5.0.0-rc.3'
     samtools_version   = '1.20'
-    stablelift_version = 'dev'    // FIXME
+    stablelift_version = '1.0.0'
 
     docker_image_bcftools = "${-> params.docker_container_registry}/bcftools-score:${params.bcftools_version}"
     docker_image_bedtools = "${-> params.docker_container_registry}/bedtools:${params.bedtools_version}"

diff --git a/config/methods.config b/config/methods.config
@@ -3,6 +3,7 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/methods/co
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/schema/schema.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/bam/bam_parser.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/store_object_as_json/store_object_as_json.config"
+includeConfig "${projectDir}/config/base.config"
 
 import nextflow.Nextflow
 
@@ -101,7 +102,6 @@ methods {
         }
 
         methods.set_output_dir()
-        methods.set_resources_allocation()
         methods.modify_base_allocations()
         methods.set_pipeline_logs()
         methods.set_env()

diff --git a/docs/pipeline-flow.puml b/docs/pipeline-flow.puml
diff --git a/docs/pipeline-flow.svg b/docs/pipeline-flow.svg
diff --git a/docs/pipeline.mmd b/docs/pipeline.mmd
@@ -30,9 +30,9 @@ flowchart TD
   --> pipeval:::linux
   --> sv_vs_snv{{Variant Type?}}
 
-  sv_vs_snv ------> r_liftover
-  header_contigs .-> r_liftover
-  chain_file2 ..-> r_liftover
+  sv_vs_snv ------> r_extract_sv
+  header_contigs .-> r_extract_sv
+  chain_file2 ..-> r_extract_sv
   gnomad_rds .-> r_extract_sv
 
   subgraph SV ["`**SV**`"]
@@ -41,8 +41,7 @@ flowchart TD
     chain_file2([chain_file]):::input
     gnomad_rds([gnomad_rds]):::input
 
-    r_liftover[liftover-Delly2-vcf.R]:::R
-    ---> r_extract_sv[extract-VCF-features-SV.R]:::R
+    r_extract_sv[extract-VCF-features-SV.R]:::R
 
   end
 
@@ -64,7 +63,7 @@ flowchart TD
         --> bcftools_annotate2["`bcftools annotate*Trinucleotide*`"]:::bcftools
     end
 
-    blocknote["`**Note:** Annotation is performed prior to LiftOver when converting from GRCh38 -> GRCh37`"]
+    blocknote["`**Note:** Annotation is performed prior to LiftOver when converting from GRCh38 to GRCh37`"]
 
     bcftools_liftover ---> gatk_func
     bcftools_annotate2 --> r_extract_snv[extract-VCF-features.R]:::R

diff --git a/docs/pipeline.mmd.svg b/docs/pipeline.mmd.svg
diff --git a/docs/stablelift-overview.png b/docs/stablelift-overview.png
diff --git a/docs/stablelift-overview.svg b/docs/stablelift-overview.svg
diff --git a/metadata.yaml b/metadata.yaml
@@ -1,9 +1,7 @@
 ---
 category: "pipeline"
-description: "A template Nextflow pipeline for styling and standardization"
-maintainers: "Boutros Lab Infrastructure <[email protected]>"
-languages: ["Nextflow", "Docker"]
-dependencies: ["Java", "Nextflow", "Docker"]
-references: "https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189620/Guide+to+Nextflow"
-tools: ["tool_a:v1.1.0", "tool_b:v1.1.0"]
+description: "Nextflow pipeline for predicting variant stability across reference genome builds."
+maintainers: "Nicholas Wiltsie <[email protected]>, Nicholas K. Wang <[email protected]>"
+languages: ["Nextflow", "R"]
+dependencies: ["Nextflow", "R", "Docker"]
 image_name: "stablelift"
diff --git a/module/scripts/extract-VCF-features-SV.R b/module/scripts/extract-VCF-features-SV.R
@@ -254,7 +254,6 @@ all.features <- c(continuous.features, categorical.features, 'ID');
 features.dt <- features.dt[, ..all.features];
 features.dt[, (continuous.features) := lapply(.SD, as.numeric), .SDcols = continuous.features];
 features.dt[, (continuous.features) := lapply(.SD, function(x) ifelse(is.na(x), 0, x)), .SDcols = continuous.features];
-features.dt[, (categorical.features) := lapply(.SD, function(x) ifelse(is.na(x), '', x)), .SDcols = categorical.features];
 features.dt[, (categorical.features) := lapply(.SD, as.factor), .SDcols = categorical.features];
 names(features.dt) <- make.names(names(features.dt));
 

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 // Metadata
 manifest {
     name = 'pipeline-StableLift'
-    author = 'Nicholas Wiltsie'
-    description = 'A template for Nextflow pipelines'
-    version = '0.1.0'
+    author = 'Nicholas Wiltsie, Nicholas K. Wang'
+    description = 'Nextflow pipeline for predicting variant stability across reference genome builds.'
+    version = '1.0.0'
 }
-Original file line number
+Diff line change
@@ Expand Up @@
     ---
-    ## [Unreleased]
+    ## [1.0.0] - 2024-09-10
     ### Added
@@ Expand Down @@