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Added the .bai and .fai files

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 10:23:07 +02:00
parent 484c8f5dfa
commit 9df830f79d
3 changed files with 18 additions and 17 deletions
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8
modules/vardictjava/main.nf
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@ -8,12 +8,12 @@ process VARDICTJAVA {
'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(bai)
path(regions_of_interest) path(regions_of_interest)
path(reference_fasta) tuple path(reference_fasta), path(reference_fai)
output: output:
tuple val(meta), path("*.vcf"), emit: vcf tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -30,7 +30,7 @@ process VARDICTJAVA {
-th $task.cpus \\ -th $task.cpus \\
-N $prefix \\ -N $prefix \\
-G $reference_fasta \\ -G $reference_fasta \\
$regions_of_interest \\ $regions_of_interest
| gzip -c > ${prefix}.vcf.gz | gzip -c > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

12
tests/modules/vardictjava/main.nf
View file

@ -8,12 +8,16 @@ workflow test_vardictjava {
bam_input_ch = Channel.of([ bam_input_ch = Channel.of([
[ id:'test', single_end:false ], // meta map [ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]) ])
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) reference = Channel.of([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
])
VARDICTJAVA ( bam_input_ch, bed, fasta ) VARDICTJAVA ( bam_input_ch, bed, reference )
} }

15
tests/modules/vardictjava/test.yml
View file

@ -1,12 +1,9 @@
## TODO nf-core: Please run the following command to build this file: - name: vardictjava test_vardictjava
# nf-core modules create-test-yml vardictjava command: nextflow run tests/modules/vardictjava -entry test_vardictjava -c tests/config/nextflow.config
- name: "vardictjava"
command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config
tags: tags:
- "vardictjava" - vardictjava
#
files: files:
- path: "output/vardictjava/test.vcf" - path: output/vardictjava/test.vcf.gz
md5sum: e667c7caad0bc4b7ac383fd023c654fc md5sum: 2179dcaee6183495b421293f42db11b5
- path: output/vardictjava/versions.yml - path: output/vardictjava/versions.yml
md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b md5sum: aac455b8c9c9194c5fed80e4fd495b96