Merge pull request #1 from TRON-Bioinformatics/nextflow

Makes Nextflow workflow work with conda + add automated tests

.github/workflows/automated_tests.yml

@@ -0,0 +1,22 @@
+name: Automated tests
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-java@v2
+      with:
+        distribution: 'zulu' # See 'Supported distributions' for available options
+        java-version: '11'
+    - uses: conda-incubator/setup-miniconda@v2
+    - name: Install dependencies
+      run: |
+        apt-get update && apt-get --assume-yes install wget make procps software-properties-common
+        wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
+    - name: Run tests
+      run: |
+        make

.gitignore

@@ -5,3 +5,8 @@ vafator.egg-info
 **/__pycache__
 .idea
 venv-win
+.nextflow.log*
+work/
+output/
+.nextflow/
+.tox/

Makefile

@@ -0,0 +1,26 @@
+
+all : clean test check
+
+clean:
+	rm -rf output
+	#rm -rf work
+	rm -f .nextflow.log*
+	rm -rf .nextflow*
+
+
+test:
+	nextflow main.nf --help
+	echo "sample_1\t"`pwd`"/test_data/test_tumor_normal.vcf\t"`pwd`"/test_data/TESTX_S1_L001.bam\t"`pwd`"/test_data/TESTX_S1_L002.bam\n" > test_data/test_input.txt
+	echo "sample_2\t"`pwd`"/test_data/test_single_sample.vcf\t"`pwd`"/test_data/TESTX_S1_L001.bam,"`pwd`"/test_data/TESTX_S1_L002.bam\t"`pwd`"/test_data/TESTX_S1_L001.bam,"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_input.txt
+	nextflow main.nf -profile test,conda --output output/test1 --input_files test_data/test_input.txt
+	nextflow main.nf -profile test,conda --output output/test2 --input_files test_data/test_input.txt --skip_multiallelic_filter
+
+
+check:
+	test -s output/test1/sample_1/test_tumor_normal.vaf.vcf || { echo "Missing test 1 sample 1 output file!"; exit 1; }
+	test -s output/test1/sample_1/test_tumor_normal.vaf.filtered_multiallelics.vcf || { echo "Missing test 1 sample 1 output file!"; exit 1; }
+	test -s output/test1/sample_2/test_single_sample.vaf.vcf || { echo "Missing test 1 sample 2 output file!"; exit 1; }
+	test -s output/test1/sample_2/test_single_sample.vaf.filtered_multiallelics.vcf || { echo "Missing test 1 sample 1 output file!"; exit 1; }
+	test -s output/test1/sample_1/test_tumor_normal.vaf.vcf || { echo "Missing test 2 sample 1 output file!"; exit 1; }
+	test -s output/test1/sample_2/test_single_sample.vaf.vcf || { echo "Missing test 2 sample 2 output file!"; exit 1; }
+

environment.yml

@@ -0,0 +1,9 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: covigator-pipeline
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::vafator=0.3.3

main.nf

@@ -1,42 +1,8 @@
 #!/usr/bin/env nextflow
 
-params.help= false
-params.input_files = false
-params.output = false
-params.mapping_quality = false
-params.base_call_quality = false
-params.skip_multiallelic_filter = false
-
-def helpMessage() {
-    log.info"""
-Usage:
-    nextflow run main.nf --input_files input_files
-
-This workflow implements the annotation of a tumor/normal pair VCF with the
-variant allele frequencies, counts and depth of coverage extracted from the
-corresponding BAM files.
-
-Input:
-    * input_files: the path to a tab-separated values file containing in each
-    row the sample name, path to the VCF file, a comma-separated list of normal
-    BAMs and a comma-separated list of normal BAMs
-    The input file does not have header!
-    Example input file:
-    identifier	/path/to/your/file.vcf  /path/to/your/normal_replica1.bam,/path/to/your/normal_replica2.bam /path/to/your/tumor_replica1.bam,/path/to/your/tumor_replica2.bam
-
-Optional input:
-    * output: the folder where to publish output
-    * skip_multiallelic_filter: skip the filtering of multiallelics by frequency in the tumor (only highest frequency variant at the same position is kept)
-    * base_call_quality: threshold for the base call quality, only base calls with a higher value are considered (default: 29)
-    * mapping_quality: threshold for the mapping quality, only reads with a higher value are considered (default: 0)
-
-Output:
-    * Annotated VCF file
-    """
-}
 
 if (params.help) {
-    helpMessage()
+    log.info params.help_message
     exit 0
 }
 
@@ -57,9 +23,8 @@ if (params.input_files) {
 }
 
 process vafator {
-    cpus 1
-    memory '4g'
-    module 'anaconda/3/2019'
+    cpus params.cpus
+    memory params.memory
     tag "${name}"
     publishDir "${publish_dir}/${name}", mode: "copy"
 
@@ -68,26 +33,21 @@ process vafator {
 
     output:
       set val("${name}"), file("${vcf.baseName}.vaf.vcf") into annotated_vcf
-      set val("${name}"), val("${publish_dir}/${name}/${vcf.baseName}.vaf.vcf") into intermediate_output_files
 
     script:
     normal_bams_param = normal_bams?.trim() ? "--normal-bams " + normal_bams.split(",").join(" ") : ""
     tumor_bams_param = tumor_bams?.trim() ? "--tumor-bams " + tumor_bams.split(",").join(" ") : ""
     mapping_quality_param = params.mapping_quality ? "--mapping-quality " + params.mapping_quality : ""
-    base_call_quality_param = params.base_call_quality ? "--base_call-quality " + params.base_call_quality : ""
+    base_call_quality_param = params.base_call_quality ? "--base-call-quality " + params.base_call_quality : ""
     """
-    /home/priesgof/src/vafator/venv/bin/vafator --input-vcf ${vcf} --output-vcf ${vcf.baseName}.vaf.vcf ${normal_bams_param} ${tumor_bams_param} ${mapping_quality_param} ${base_call_quality_param}
+    vafator --input-vcf ${vcf} --output-vcf ${vcf.baseName}.vaf.vcf ${normal_bams_param} ${tumor_bams_param} ${mapping_quality_param} ${base_call_quality_param}
     """
 }
 
-if (params.skip_multiallelic_filter) {
-    output_files = intermediate_output_files
-}
-else {
+if (!params.skip_multiallelic_filter) {
     process multiallelic_filter {
-        cpus 1
-        memory '4g'
-        module 'anaconda/3/2019'
+        cpus params.cpus
+        memory params.memory
         tag "${name}"
         publishDir "${publish_dir}/${name}", mode: "copy"
 
@@ -100,11 +60,7 @@ else {
 
         script:
         """
-        /home/priesgof/src/vafator/venv/bin/multiallelics-filter --input-vcf ${vcf} --output-vcf ${vcf.baseName}.filtered_multiallelics.vcf
+        multiallelics-filter --input-vcf ${vcf} --output-vcf ${vcf.baseName}.filtered_multiallelics.vcf
         """
     }
 }
-
-output_files
-	.map {it.join("\t")}
-	.collectFile(name: "${publish_dir}/annotated_vcfs.txt", newLine: true)

nextflow.config

@@ -0,0 +1,73 @@
+params.cpus = 1
+params.memory = "4g"
+
+params.help= false
+params.input_files = false
+params.output = false
+params.mapping_quality = false
+params.base_call_quality = false
+params.skip_multiallelic_filter = false
+
+profiles {
+  conda { process.conda = "$baseDir/environment.yml" }
+  debug { process.beforeScript = 'echo $HOSTNAME' }
+  test {
+    params.cpus = 1
+    params.memory = "3g"
+    timeline.enabled = false
+    report.enabled = false
+    trace.enabled = false
+    dag.enabled = false
+  }
+}
+
+// Export this variable to prevent local Python libraries from conflicting with those in the container
+env {
+  PYTHONNOUSERSITE = 1
+}
+
+// Capture exit codes from upstream processes when piping
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+
+cleanup = true
+conda.createTimeout = '1 h'
+
+VERSION = '0.3.4'
+
+manifest {
+  name = 'TRON-Bioinformatics/vafator'
+  author = 'Pablo Riesgo-Ferreiro'
+  homePage = 'https://github.com/TRON-Bioinformatics/vafator'
+  description = 'A tool to annotate VCF files with variant allele frequencies and depth of coverage'
+  mainScript = 'main.nf'
+  nextflowVersion = '>=19.10.0'
+  version = VERSION
+}
+
+params.help_message = """
+VAFator $VERSION
+
+Usage:
+    nextflow run main.nf --input_files input_files
+
+This workflow implements the annotation of a tumor/normal pair VCF with the
+variant allele frequencies, counts and depth of coverage extracted from the
+corresponding BAM files.
+
+Input:
+    * input_files: the path to a tab-separated values file containing in each
+    row the sample name, path to the VCF file, a comma-separated list of normal
+    BAMs and a comma-separated list of normal BAMs
+    The input file does not have header!
+    Example input file:
+    identifier	/path/to/your/file.vcf  /path/to/your/normal_replica1.bam,/path/to/your/normal_replica2.bam /path/to/your/tumor_replica1.bam,/path/to/your/tumor_replica2.bam
+
+Optional input:
+    * output: the folder where to publish output
+    * skip_multiallelic_filter: skip the filtering of multiallelics by frequency in the tumor (only highest frequency variant at the same position is kept)
+    * base_call_quality: threshold for the base call quality, only base calls with a higher value are considered (default: 29)
+    * mapping_quality: threshold for the mapping quality, only reads with a higher value are considered (default: 0)
+
+Output:
+    * Annotated VCF file
+    """

test_data/input_data.txt

@@ -0,0 +1,2 @@
+sample1	test_data/test_tumor_normal.vcf	test_data/TESTX_S1_L001.bam	test_data/TESTX_S1_L002.bam
+sample2	test_data/test_single_sample.vcf	test_data/TESTX_S1_L001.bam,test_data/TESTX_S1_L002.bam	test_data/TESTX_S1_L001.bam,test_data/TESTX_S1_L002.bam

test_data/test_input.txt

@@ -0,0 +1,3 @@
+sample_1	/home/priesgo/src/github/vafator/test_data/test_tumor_normal.vcf	/home/priesgo/src/github/vafator/test_data/TESTX_S1_L001.bam	/home/priesgo/src/github/vafator/test_data/TESTX_S1_L002.bam
+
+sample_2	/home/priesgo/src/github/vafator/test_data/test_single_sample.vcf	/home/priesgo/src/github/vafator/test_data/TESTX_S1_L001.bam,/home/priesgo/src/github/vafator/test_data/TESTX_S1_L002.bam	/home/priesgo/src/github/vafator/test_data/TESTX_S1_L001.bam,/home/priesgo/src/github/vafator/test_data/TESTX_S1_L002.bam

test_data/test_single_sample.vcf

@@ -0,0 +1,39 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">
+##FILTER=<ID=NOT_PASSED,Description="whatever">
+##FILTER=<ID=MULTIALLELIC,Description="whatever">
+##FILTER=<ID=UNTRIMMED,Description="whatever">
+##FILTER=<ID=UNALIGNED,Description="whatever">
+##FILTER=<ID=UNALIGNED-UNTRIMMED,Description="whatever">
+##FILTER=<ID=MNV,Description="whatever">
+##FILTER=<ID=MNV-INDEL,Description="whatever">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
+chr1	13082	.	C	A	.	NOT_PASSED		GT:AD	0/1:76,1
+chr1	13081	.	A	C	.	NOT_PASSED		GT:AD	0/1:37,1
+chr1	13202	.	A	G	.	NOT_PASSED		GT:AD	0/1:107,26
+chr1	13201	.	T	G	.	NOT_PASSED		GT:AD	0/1:35,3
+chr1	13201	.	T	C	.	PASS		GT:AD	0/1:196,24
+chr1	13263	.	T	C	.	PASS		GT:AD	0/1:136,31
+chr1	13083	.	A	C	.	PASS		GT:AD	0/1:260,18
+chr1	13263	.	TCC	CCC	.	UNTRIMMED		GT:AD	0/1:136,31
+chr1	13083	.	AGA	AGC	.	UNTRIMMED		GT:AD	0/1:260,18
+chr1	13141	.	C	AAAAAC	.	UNALIGNED		GT:AD	0/1:76,14
+chr1	13141	.	CT	AAAAACT	.	UNALIGNED-UNTRIMMED		GT:AD	0/1:76,14
+chr1	13141	.	CTGAGG	G	.	UNALIGNED		GT:AD	0/1:76,14
+chr1	13141	.	CTGAGG	GG	.	UNALIGNED-UNTRIMMED		GT:AD	0/1:76,14
+chr1	13081	.	ACAG	CCAC	.	MNV		GT:AD	0/1:76,14
+chr1	13141	.	CTGAGG	ATGAGT	.	MNV		GT:AD	0/1:37,5
+chr1	13201	.	TAGCCT	GAGCCC	.	MNV		GT:AD	0/1:107,26
+chr1	13261	.	GCTCCT	CCCCCC	.	MNV		GT:AD	0/1:35,3
+chr1	13321	.	AGCCCT	CGCC	.	MNV-INDEL		GT:AD	0/1:196,24
+chr1	13081	.	ACA	GCAAAAA	.	MNV-INDEL		GT:AD	0/1:196,24
+chr1	13204	.	C	G,T	.	MULTIALLELIC		GT:AD	0/1:196,24,1
+chr1	13324	.	C	G,T	.	MULTIALLELIC		GT:AD	1/2:196,24,1
+chr1	13262	.	C	G,T,A	.	MULTIALLELIC		GT:AD	2/3:196,24,1,1
+chr1	13323	.	C	A,G,T	.	MULTIALLELIC		GT:AD	2/3:196,24,1,1

test_data/test_tumor_normal.vcf

@@ -0,0 +1,39 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="Accept as a confident somatic mutation">
+##FILTER=<ID=NOT_PASSED,Description="whatever">
+##FILTER=<ID=MULTIALLELIC,Description="whatever">
+##FILTER=<ID=UNTRIMMED,Description="whatever">
+##FILTER=<ID=UNALIGNED,Description="whatever">
+##FILTER=<ID=UNALIGNED-UNTRIMMED,Description="whatever">
+##FILTER=<ID=MNV,Description="whatever">
+##FILTER=<ID=MNV-INDEL,Description="whatever">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##contig=<ID=chr1,length=249250621,assembly=hg19>
+##contig=<ID=chr2,length=243199373,assembly=hg19>
+##contig=<ID=chr3,length=198022430,assembly=hg19>
+##contig=<ID=chr4,length=191154276,assembly=hg19>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
+chr1	13082	.	C	A	.	NOT_PASSED		GT:AD	0:80,1	0/1:76,1
+chr1	13081	.	A	C	.	NOT_PASSED		GT:AD	0:62,0	0/1:37,1
+chr1	13202	.	A	G	.	NOT_PASSED		GT:AD	0:157,0	0/1:107,26
+chr1	13201	.	T	G	.	NOT_PASSED		GT:AD	0:41,0	0/1:35,3
+chr1	13201	.	T	C	.	PASS		GT:AD	0:229,1	0/1:196,24
+chr1	13263	.	T	C	.	PASS		GT:AD	0:229,0	0/1:136,31
+chr1	13083	.	A	C	.	PASS		GT:AD	0:276,0	0/1:260,18
+chr1	13263	.	TCC	CCC	.	UNTRIMMED		GT:AD	0:229,0	0/1:136,31
+chr1	13083	.	AGA	AGC	.	UNTRIMMED		GT:AD	0:276,0	0/1:260,18
+chr1	13141	.	C	AAAAAC	.	UNALIGNED		GT:AD	0:80,1	0/1:76,14
+chr1	13141	.	CT	AAAAACT	.	UNALIGNED-UNTRIMMED		GT:AD	0:80,1	0/1:76,14
+chr1	13141	.	CTGAGG	G	.	UNALIGNED		GT:AD	0:80,1	0/1:76,14
+chr1	13141	.	CTGAGG	GG	.	UNALIGNED-UNTRIMMED		GT:AD	0:80,1	0/1:76,14
+chr1	13081	.	ACAG	CCAC	.	MNV		GT:AD	0:80,1	0/1:76,14
+chr1	13141	.	CTGAGG	ATGAGT	.	MNV		GT:AD	0:62,0	0/1:37,5
+chr1	13201	.	TAGCCT	GAGCCC	.	MNV		GT:AD	0:157,0	0/1:107,26
+chr1	13261	.	GCTCCT	CCCCCC	.	MNV		GT:AD	0:41,0	0/1:35,3
+chr1	13321	.	AGCCCT	CGCC	.	MNV-INDEL		GT:AD	0:229,1	0/1:196,24
+chr1	13081	.	ACA	GCAAAAA	.	MNV-INDEL		GT:AD	0:229,1	0/1:196,24
+chr1	13204	.	C	G,T	.	MULTIALLELIC		GT:AD	1:229,1,1	0/1:196,24,1
+chr1	13324	.	C	G,T	.	MULTIALLELIC		GT:AD	0:229,1,1	1/2:196,24,1
+chr1	13262	.	C	G,T,A	.	MULTIALLELIC		GT:AD	1:229,1,1,1	2/3:196,24,1,1
+chr1	13323	.	C	A,G,T	.	MULTIALLELIC		GT:AD	1:229,1,1,1	2/3:196,24,1,1

vafator/__init__.py

@@ -1 +1 @@
-VERSION='0.3.3'
+VERSION='0.3.4'

vafator/tests/resources/results/test1_output.vcf

@@ -8,7 +8,7 @@
 ##contig=<ID=chr6,length=171115067>
 ##INFO=<ID=tumor_af,Number=1,Type=String,Description="">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##vafator_command_line={"name": "multiallelic-filter", "version": "0.2.2", "date": "Thu Sep 30 22:02:41 2021", "timestamp": 1633032161.547325, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test1_output.vcf"}
+##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.1", "date": "Thu Oct  7 22:21:54 2021", "timestamp": 1633638114.027123, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test1.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test1_output.vcf"}
 ##INFO=<ID=multiallelic,Number=.,Type=String,Description="Indicates multiallelic variants filtered and their frequencies if any (e.g.: T,0.12)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
 chr1	25734793	.	C	T	.	PASS	.	GT	0/1

vafator/tests/resources/results/test2_output.vcf

@@ -8,7 +8,7 @@
 ##contig=<ID=chr6,length=171115067>
 ##INFO=<ID=tumor_af,Number=1,Type=String,Description="">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##vafator_command_line={"name": "multiallelic-filter", "version": "0.2.2", "date": "Thu Sep 30 22:02:41 2021", "timestamp": 1633032161.547325, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test2.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test2_output.vcf"}
+##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.1", "date": "Thu Oct  7 22:21:54 2021", "timestamp": 1633638114.027123, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test2.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test2_output.vcf"}
 ##INFO=<ID=multiallelic,Number=.,Type=String,Description="Indicates multiallelic variants filtered and their frequencies if any (e.g.: T,0.12)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
 chr1	25734793	.	C	T	.	PASS	.	GT	0/1

vafator/tests/resources/results/test3_output.vcf

@@ -8,7 +8,7 @@
 ##contig=<ID=chr6,length=171115067>
 ##INFO=<ID=tumor_af,Number=1,Type=String,Description="">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##vafator_command_line={"name": "multiallelic-filter", "version": "0.2.2", "date": "Thu Sep 30 22:02:41 2021", "timestamp": 1633032161.547325, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test3.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test3_output.vcf"}
+##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.1", "date": "Thu Oct  7 22:21:54 2021", "timestamp": 1633638114.027123, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test3.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test3_output.vcf"}
 ##INFO=<ID=multiallelic,Number=.,Type=String,Description="Indicates multiallelic variants filtered and their frequencies if any (e.g.: T,0.12)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
 chr1	1234	.	C	T	.	PASS	.	GT	0/1

vafator/tests/resources/results/test4_output.vcf

@@ -8,7 +8,7 @@
 ##contig=<ID=chr6,length=171115067>
 ##INFO=<ID=tumor_af,Number=1,Type=String,Description="">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##vafator_command_line={"name": "multiallelic-filter", "version": "0.2.2", "date": "Thu Sep 30 22:02:41 2021", "timestamp": 1633032161.547325, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test4.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test4_output.vcf"}
+##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.1", "date": "Thu Oct  7 22:21:54 2021", "timestamp": 1633638114.027123, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test4.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test4_output.vcf"}
 ##INFO=<ID=multiallelic,Number=.,Type=String,Description="Indicates multiallelic variants filtered and their frequencies if any (e.g.: T,0.12)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
 chr4	1235	.	C	A	.	PASS	tumor_af=0.2;multiallelic=,G,0.15	GT	0/1

vafator/tests/resources/results/test5_output.vcf

@@ -8,7 +8,7 @@
 ##contig=<ID=chr6,length=171115067>
 ##INFO=<ID=tumor_af,Number=1,Type=String,Description="">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##vafator_command_line={"name": "multiallelic-filter", "version": "0.2.2", "date": "Thu Sep 30 22:02:41 2021", "timestamp": 1633032161.547325, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test5.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test5_output.vcf"}
+##vafator_command_line={"name": "multiallelic-filter", "version": "0.3.1", "date": "Thu Oct  7 22:21:54 2021", "timestamp": 1633638114.027123, "input_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/test5.vcf", "output_vcf": "/home/priesgo/src/github/vafator/vafator/tests/resources/results/test5_output.vcf"}
 ##INFO=<ID=multiallelic,Number=.,Type=String,Description="Indicates multiallelic variants filtered and their frequencies if any (e.g.: T,0.12)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
-chr4	1235	.	C	G	.	PASS	tumor_af=0.1;multiallelic=,T,0.1,A,0.1	GT	0/1
+chr4	1235	.	C	A	.	PASS	tumor_af=0.1;multiallelic=,G,0.1	GT	0/1