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Added the statistical tests and conversion to vcf

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 15:33:27 +02:00
parent 6678ad4426
commit bdff37c3d7
3 changed files with 8 additions and 2 deletions
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7
modules/vardictjava/main.nf
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@ -21,17 +21,22 @@ process VARDICTJAVA {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args_conversion = task.ext.args_conversion ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
vardict-java \\ vardict-java \\
$args \\ $args \\
-c 1 -S 2 -E 3 -h \\ -c 1 -S 2 -E 3 \\
-b $bam \\ -b $bam \\
-th $task.cpus \\ -th $task.cpus \\
-N $prefix \\ -N $prefix \\
-G $reference_fasta \\ -G $reference_fasta \\
$regions_of_interest \\ $regions_of_interest \\
| teststrandbias.R \\
| var2vcf_valid.pl \\
$args_conversion \\
-N $prefix \\
| gzip -c > ${prefix}.vcf.gz | gzip -c > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

1
tests/modules/vardictjava/nextflow.config
View file

@ -4,5 +4,6 @@ process {
withName: VARDICTJAVA { withName: VARDICTJAVA {
ext.args = '' ext.args = ''
ext.args_conversion = ''
} }
} }

2
tests/modules/vardictjava/test.yml
View file

@ -4,6 +4,6 @@
- vardictjava - vardictjava
files: files:
- path: output/vardictjava/test.vcf.gz - path: output/vardictjava/test.vcf.gz
md5sum: 2179dcaee6183495b421293f42db11b5 md5sum: 3f1f227afc532bddeb58f16fd3013fc8
- path: output/vardictjava/versions.yml - path: output/vardictjava/versions.yml
md5sum: aac455b8c9c9194c5fed80e4fd495b96 md5sum: aac455b8c9c9194c5fed80e4fd495b96