feat: update delly container (#950)

* update changelog * update delly * add command to container tests
Clinical-Genomics · Jun 9, 2022 · de86371 · de86371
1 parent b8998d8
commit de86371
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Showing 5 changed files with 8 additions and 5 deletions.
diff --git a/BALSAMIC/containers/delly/Dockerfile b/BALSAMIC/containers/delly/Dockerfile
@@ -22,6 +22,7 @@ RUN apt-get update && apt-get install -y \
     libncurses-dev \
     liblzma-dev \
     zlib1g-dev \
+    bcftools \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
@@ -34,7 +35,7 @@ ENV OMP_NUM_THREADS 2
 RUN cd /opt \
     && git clone --recursive https://github.com/dellytools/delly.git \
     && cd /opt/delly/ \
-    && git checkout v0.9.1 \
+    && git checkout v1.0.3 \
     && make STATIC=1 PARALLEL=1 all \
     && make install \
 
diff --git a/BALSAMIC/containers/delly/delly.yaml b/BALSAMIC/containers/delly/delly.yaml
@@ -1 +1 @@
-- delly=0.9.1
+- delly=1.0.3
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -5,7 +5,7 @@ Added:
 ^^^^^^
 
 * New option `analysis-workflow` to balsamic config case CLI https://github.com/Clinical-Genomics/BALSAMIC/pull/932
-* Delly TIDDIT and vcf2cytosure for WGS https://github.com/Clinical-Genomics/BALSAMIC/pull/947
+* `Delly` `TIDDIT` `vcf2cytosure` and method to process SVs and CNVs for WGS https://github.com/Clinical-Genomics/BALSAMIC/pull/947
 
 Changed:
 ^^^^^^^^
@@ -15,6 +15,8 @@ Changed:
 * QC-workflow for panel cases to be run only with `balsamic-qc` https://github.com/Clinical-Genomics/BALSAMIC/pull/942
 * `get_snakefile` function takes the argument `analysis_workflow` to trigger the QC workflow when necessary https://github.com/Clinical-Genomics/BALSAMIC/pull/942
 * `bcftools_counts` input depending on `analysis_workflow` https://github.com/Clinical-Genomics/BALSAMIC/pull/942
+* Update `delly` to v1.0.3 https://github.com/Clinical-Genomics/BALSAMIC/pull/950
+
 
 Fixed:
 ^^^^^^

diff --git a/container_tests/delly/delly.sh b/container_tests/delly/delly.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Test if commands exist
 
-valid_commands=( "delly" )
+valid_commands=( "delly" "bcftools" )
 
 for valid_command in "${valid_commands[@]}"
 do

diff --git a/container_tests/varcall_py3/varcall_py3.sh b/container_tests/varcall_py3/varcall_py3.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Test if commands exist
 
-valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb")
+valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb" "bwa" "tiddit")
 
 for valid_command in "${valid_commands[@]}"
 do