Update echtvar (#306)

* Update echtvar

* Add README and Dockerfile

CHANGELOG.md

@@ -52,6 +52,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#277](https://github.com/genomic-medicine-sweden/nallo/pull/277) - Allowed CNV calling as soon as SNV calling for a sample is finished
 - [#278](https://github.com/genomic-medicine-sweden/nallo/pull/278) - Changed the SNV ranking to run in parallel per region
 - [#300](https://github.com/genomic-medicine-sweden/nallo/pull/300) - Clarified and formatted nallo.nf
+- [#306](https://github.com/genomic-medicine-sweden/nallo/pull/306) - Updated echtvar version
 
 ### `Removed`
 
@@ -97,6 +98,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | htslib      | 1.19.1      | 1.20        |
 | cadd        |             | 1.6.post1   |
 | gawk        |             | 5.3.0       |
+| echtvar     | 0.1.7       | 0.2.0       |
 
 ## v0.2.0 - [2024-06-26]
 

modules/local/echtvar/anno/Dockerfile

@@ -0,0 +1,11 @@
+# syntax=docker/dockerfile:1
+FROM ubuntu:22.04
+
+USER root
+
+RUN apt-get update && apt-get install -y procps sed && rm -rf /var/lib/apt/lists/*
+# install app
+COPY echtvar /usr/bin/echtvar
+
+# final configuration
+ENV FLASK_APP=echtvar

modules/local/echtvar/anno/README.md

@@ -0,0 +1,8 @@
+This docker was created with the following commands:
+
+```bash
+wget https://github.com/brentp/echtvar/releases/download/v0.2.0/echtvar
+chmod +x echtvar
+docker build . -t fellen31/echtvar:0.2.0
+docker push fellen31/echtvar:0.2.0
+```

modules/local/echtvar/anno/main.nf

@@ -2,7 +2,7 @@ process ECHTVAR_ANNO {
     tag "$meta.id"
     label 'process_single'
 
-    container "docker.io/fellen31/echtvar:latest"
+    container "docker.io/fellen31/echtvar:0.2.0"
 
     input:
     tuple val(meta),  path(vcf)

modules/local/echtvar/encode/Dockerfile

@@ -0,0 +1,11 @@
+# syntax=docker/dockerfile:1
+FROM ubuntu:22.04
+
+USER root
+
+RUN apt-get update && apt-get install -y procps sed && rm -rf /var/lib/apt/lists/*
+# install app
+COPY echtvar /usr/bin/echtvar
+
+# final configuration
+ENV FLASK_APP=echtvar

modules/local/echtvar/encode/README.md

@@ -0,0 +1,8 @@
+This docker was created with the following commands:
+
+```bash
+wget https://github.com/brentp/echtvar/releases/download/v0.2.0/echtvar
+chmod +x echtvar
+docker build . -t fellen31/echtvar:0.2.0
+docker push fellen31/echtvar:0.2.0
+```

modules/local/echtvar/encode/main.nf

@@ -2,7 +2,7 @@ process ECHTVAR_ENCODE {
     tag "$meta.id"
     label 'process_single'
 
-    container "docker.io/fellen31/echtvar:latest"
+    container "docker.io/fellen31/echtvar:0.2.0"
 
     input:
     tuple val(meta), path(bcf)

subworkflows/local/snv_annotation/tests/main.nf.test

@@ -102,8 +102,8 @@ nextflow_workflow {
                 { assert snapshot(
                     workflow.out.versions,
                     file(workflow.out.tbi.get(0).get(1)).name,
-                    path(workflow.out.vcf.get(0).get(1)).linesGzip[47..118], // Stable
-                    path(workflow.out.vcf.get(0).get(1)).linesGzip[120..150] // Stable
+                    path(workflow.out.vcf.get(0).get(1)).linesGzip[48..118], // Stable
+                    path(workflow.out.vcf.get(0).get(1)).linesGzip[121..150] // Stable
                 ).match() }
             )
         }