Added potentially missing dependency of hexdump

CHANGELOG.md

@@ -4,8 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
-
+## [0.5.0] - 2021-01-08
 ### Changed
 - merge_vcf_files.py now sets genotypes with a DHFFC of Inf, Nan, or higher than 4 to missing
 - vcf_to_table.py now writes both samples and genotypes into the SAMPLES-VAR column, as opposed to samples only
@@ -15,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Option to merge_vcf_files.py to specify read depth cutoffs for calling deletions and duplications
 - Option to merge_vcf_files.py to generate output that can be processed by [svtyper](https://github.com/hall-lab/svtyper)
 - Nextflow scripts to convert output BEDPEs to VCFs and add read depth information to each call using duphold (script heavily inspired by [methylseq](https://github.com/nf-core/methylseq))
+- Potentially missing hexdump dependency to Dockerfile
 
 ## [0.4.0] - 2020-04-14
 ### Added

docker/Dockerfile

@@ -8,7 +8,7 @@ CMD ["/sbin/my_init"]
 
 # Install basic applications
 RUN apt-get update && \
-	apt-get install -y curl gcc g++ wget git unzip tar gzip bzip2 xz-utils pigz make zlib1g-dev libncurses5-dev openjdk-8-jdk ant ca-certificates ca-certificates-java && \
+	apt-get install -y curl gcc g++ wget git unzip tar gzip bzip2 xz-utils pigz make zlib1g-dev libncurses5-dev openjdk-8-jdk ant ca-certificates ca-certificates-java bsdmainutils && \
 	apt-get clean && \
 	update-ca-certificates -f && \
 	rm -rf /var/lib/apt/lists/* && \ 
@@ -64,7 +64,7 @@ RUN source activate hecaton_py2 && \
 # RUN git clone https://git.wur.nl/wijfj001/hecaton.git && cd hecaton && \
 #	git checkout e85bba0c && cd .. && \
 RUN git clone https://git.wur.nl/bioinformatics/hecaton.git && \
-	echo "f82885e8" && \
+	echo "aeb7ff36" && \
 	chmod +x hecaton/scripts/collapse/* && \
 	chmod +x hecaton/scripts/convert/* && \
 	chmod +x hecaton/scripts/filter/* && \

nextflow/hecaton.nf

@@ -5,7 +5,7 @@
  *@authors
  *Raúl Wijfjes <raul.wijfjes@wur.nl>
  *
- *Date last modified: 16-12-2019
+ *Date last modified: 08-01-2021
  */
 
 params.genome_file = ""
@@ -25,7 +25,7 @@ params.help = false
 def helpMessage() {
     log.info"""
     =========================================
-     Hecaton v0.4.0
+     Hecaton v0.5.0
     =========================================
     Usage:
     nextflow run hecaton --genome_file reference.fa --reads "prefix_{1,2}.fastq" --manta_config configManta_weight_1.py.ini --model_file model_file.pkl --output_dir results

nextflow/hecaton_no_align.nf

@@ -5,7 +5,7 @@
  *@authors
  *Raúl Wijfjes <raul.wijfjes@wur.nl>
  *
- *Date last modified: 16-12-2019
+ *Date last modified: 08-01-2021
  */
 
 params.genome_file = ""
@@ -25,7 +25,7 @@ params.help = false
 def helpMessage() {
     log.info"""
     =========================================
-     Hecaton v0.4.0
+     Hecaton v0.5.0
     =========================================
     Usage:
     nextflow run hecaton --genome_file reference.fa --bwa_bams "*.bam" --manta_config configManta_weight_1.py.ini --model_file model_file.pkl --output_dir results

tests/functional_test_docker.sh

@@ -4,7 +4,7 @@ set -e
 
 mkdir -p test_wd_docker && cd test_wd_docker && \
 
-nextflow run -w functional_workdir -with-docker hecaton:v0.3.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton.nf \
+nextflow run -w functional_workdir -with-docker hecaton:v0.4.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton.nf \
 	--genome_file ../tests/functional/test.fa \
 	--reads "../tests/functional/test{1,2}.fq.gz" \
 	--model_file ../models/random_forest_model_concat_A_thaliana_ColxCvi_O_sativa_Suijing18_coverage_10x_insertions_balanced_subsample.pkl \
@@ -14,7 +14,7 @@ nextflow run -w functional_workdir -with-docker hecaton:v0.3.0 -c ../nextflow/ne
 	--output_dir test_o && \
 	echo "Functional test with non-empty input successful" && \
 
-nextflow run -w functional_workdir_empty -with-docker hecaton:v0.3.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton.nf \
+nextflow run -w functional_workdir_empty -with-docker hecaton:v0.4.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton.nf \
 	--genome_file ../tests/functional/test.fa \
 	--reads "../tests/functional/test_empty{1,2}.fq.gz" \
 	--model_file ../models/random_forest_model_concat_A_thaliana_ColxCvi_O_sativa_Suijing18_coverage_10x_insertions_balanced_subsample.pkl \
@@ -24,7 +24,7 @@ nextflow run -w functional_workdir_empty -with-docker hecaton:v0.3.0 -c ../nextf
 	--output_dir test_o_empty && \
 	echo "Functional test with empty input successful" && \
 
-nextflow run -w functional_workdir_no_align -with-docker hecaton:v0.3.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton_no_align.nf \
+nextflow run -w functional_workdir_no_align -with-docker hecaton:v0.4.0 -c ../nextflow/nextflow.config -resume ../nextflow/hecaton_no_align.nf \
 	--genome_file ../tests/functional/test.fa \
 	--bwa_bams "../tests/functional/test.bam" \
 	--model_file ../models/random_forest_model_concat_A_thaliana_ColxCvi_O_sativa_Suijing18_coverage_10x_insertions_balanced_subsample.pkl \