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small changes to vcfanno (#1804)

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removed a redundant input field from vcfanno

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
This commit is contained in:
nvnieuwk 2022-06-24 08:58:26 +02:00 committed by GitHub
parent 5e2325956c
commit 1363130410
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 16 additions and 23 deletions
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4
modules/vcfanno/main.nf
View file

@ -9,7 +9,6 @@ process VCFANNO {
input: input:
tuple val(meta), path(vcf), path(tbi) tuple val(meta), path(vcf), path(tbi)
tuple val(meta), path(vcf_uncompressed)
path toml path toml
path resource_dir path resource_dir
@ -23,7 +22,6 @@ process VCFANNO {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_vcf = vcf_uncompressed ?: vcf
""" """
ln -sf $resource_dir/* \$(pwd) ln -sf $resource_dir/* \$(pwd)
@ -31,7 +29,7 @@ process VCFANNO {
-p $task.cpus \\ -p $task.cpus \\
$args \\ $args \\
$toml \\ $toml \\
$input_vcf \\ $vcf \\
> ${prefix}_annotated.vcf > ${prefix}_annotated.vcf
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

15
tests/modules/vcfanno/main.nf
View file

@ -13,29 +13,24 @@ workflow test_vcfanno {
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
] ]
input_2 = [ [ id:'test_compressed', single_end:false ], // meta map
[] ]
toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ] resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
UNTAR ( resource_dir ) UNTAR ( resource_dir )
VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } ) VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
} }
workflow test_vcfanno_uncompressed { workflow test_vcfanno_uncompressed {
input = [ [ id:'test_uncompressed', single_end:false ], // meta map input = [
[] ,[] ]
input_2 = [
[ id:'test_uncompressed', single_end:false ], // meta map [ id:'test_uncompressed', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
] ]
toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ] resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
UNTAR ( resource_dir ) UNTAR ( resource_dir )
VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } ) VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
} }

20
tests/modules/vcfanno/test.yml
View file

@ -1,23 +1,23 @@
- name: vcfanno test_vcfanno - name: vcfanno test_vcfanno
command: nextflow run tests/modules/vcfanno -entry test_vcfanno -c tests/config/nextflow.config command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config -c ./tests/modules/vcfanno/nextflow.config
tags: tags:
- vcfanno - vcfanno
files: files:
- path: output/untar/versions.yml - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
md5sum: 6de038155bccbe4d264d09529bf9f4d8 md5sum: eba4b55d81148d9c316cda68a5c0ad6d
- path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
- path: output/vcfanno/test_compressed_annotated.vcf - path: output/vcfanno/test_compressed_annotated.vcf
md5sum: 90ceb2fd2e06e781846d69c3981db665 md5sum: 90ceb2fd2e06e781846d69c3981db665
- path: output/vcfanno/versions.yml
md5sum: 62d13540503b22f04a2280c91942cb03
- name: vcfanno test_vcfanno_uncompressed - name: vcfanno test_vcfanno_uncompressed
command: nextflow run tests/modules/vcfanno -entry test_vcfanno_uncompressed -c tests/config/nextflow.config command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config -c ./tests/modules/vcfanno/nextflow.config
tags: tags:
- vcfanno - vcfanno
files: files:
- path: output/untar/versions.yml - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
md5sum: a0de70274caac0cca31b077a1e7172d9 md5sum: eba4b55d81148d9c316cda68a5c0ad6d
- path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
- path: output/vcfanno/test_uncompressed_annotated.vcf - path: output/vcfanno/test_uncompressed_annotated.vcf
md5sum: 90ceb2fd2e06e781846d69c3981db665 md5sum: 90ceb2fd2e06e781846d69c3981db665
- path: output/vcfanno/versions.yml
md5sum: 300218dad68c3ffcc4783daa4f7c5a43