install python differently

.gitlab-ci.yml

@@ -4,10 +4,8 @@ image: openjdk:8u292-jre-buster
 before_script:
   - java -version
   - apt-get update && apt-get --assume-yes install wget make procps software-properties-common
-  #- add-apt-repository --yes ppa:deadsnakes/ppa
-  #- apt-get -yq update
-  - apt-get --assume-yes install python3 python3-pip
-  - pip3 install biopython==1.76
+  #- apt-get --assume-yes install python3 python3-pip
+  #- pip3 install biopython==1.76
   - wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
   - nextflow help
   - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Makefile

@@ -7,24 +7,24 @@ clean:
 	rm -rf .nextflow*
 
 test:
-	#nextflow main.nf --help
-	#nextflow main.nf -profile test,conda --initialize
-	#nextflow main.nf -profile test,conda --name ERR4145453 \
-	#--output output/test1 \
-	#--fastq1 test_data/ERR4145453_1.fastq.gz \
-	#--fastq2 test_data/ERR4145453_2.fastq.gz
-	#nextflow main.nf -profile test,conda --name ERR4145453 \
-	#--output output/test2 \
-	#--fastq1 test_data/ERR4145453_1.fastq.gz --keep_intermediate
-	#nextflow main.nf -profile test,conda --name ERR4145453 \
-	#--output output/test3 \
-	#--fastq1 test_data/ERR4145453_1.fastq.gz \
-	#--fastq2 test_data/ERR4145453_2.fastq.gz \
-	#--keep_intermediate
-	#nextflow main.nf -profile test,conda --name hCoV-19_NTXX \
-	#--output output/test4 \
-	#--fasta test_data/hCoV-19_NTXX.fasta
-	python3 -m unittest bin/test_assembly_variant_caller.py
+	nextflow main.nf --help
+	nextflow main.nf -profile test,conda --initialize
+	nextflow main.nf -profile test,conda --name ERR4145453 \
+	--output output/test1 \
+	--fastq1 test_data/ERR4145453_1.fastq.gz \
+	--fastq2 test_data/ERR4145453_2.fastq.gz
+	nextflow main.nf -profile test,conda --name ERR4145453 \
+	--output output/test2 \
+	--fastq1 test_data/ERR4145453_1.fastq.gz --keep_intermediate
+	nextflow main.nf -profile test,conda --name ERR4145453 \
+	--output output/test3 \
+	--fastq1 test_data/ERR4145453_1.fastq.gz \
+	--fastq2 test_data/ERR4145453_2.fastq.gz \
+	--keep_intermediate
+	nextflow main.nf -profile test,conda --name hCoV-19_NTXX \
+	--output output/test4 \
+	--fasta test_data/hCoV-19_NTXX.fasta
+	#python3 -m unittest bin/test_assembly_variant_caller.py
 
 check:
 	test -s output/test1/ERR4145453/ERR4145453.bcftools.normalized.annotated.vcf.gz || { echo "Missing test 1 VCF output file!"; exit 1; }