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Passing test

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Thiseas Christos Lamnidis 2022-04-29 15:07:32 +02:00
parent bad832c2ea
commit 4317ad85ae
4 changed files with 20 additions and 11 deletions
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2
modules/sexdeterrmine/main.nf
View file

@ -23,6 +23,8 @@ process SEXDETERRMINE {
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 sample_list = sample_list_file ? '-f ${sample_list_file}' : '' def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
""" """
sexdeterrmine \\ sexdeterrmine \\
-I $depth \\ -I $depth \\

2
tests/modules/sexdeterrmine/main.nf
View file

@ -9,7 +9,7 @@ workflow test_sexdeterrmine {
input = [ input = [
[ id:'test', single_end:false ], // meta map [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ] file("https://github.com/nf-core/test-datasets/raw/eager/testdata/Human/bam/JK2067_downsampled_s0.1.bam", checkIfExists: true) ]
SAMTOOLS_DEPTH ( input ) SAMTOOLS_DEPTH ( input )
SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] ) SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )

6
tests/modules/sexdeterrmine/nextflow.config
View file

@ -3,6 +3,10 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:SAMTOOLS_DEPTH { withName:SAMTOOLS_DEPTH {
ext.args = "-aa -H" ext.args = "-H"
}
withName:SEXDETERRMINE {
ext.prefix = { "${meta.id}_sexdet" }
} }
} }

21
tests/modules/sexdeterrmine/test.yml
View file

@ -1,12 +1,15 @@
## TODO nf-core: Please run the following command to build this file: - name: sexdeterrmine test_sexdeterrmine
# nf-core modules create-test-yml sexdeterrmine command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
- name: "sexdeterrmine"
command: nextflow run ./tests/modules/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config -c ./tests/modules/sexdeterrmine/nextflow.config
tags: tags:
- "sexdeterrmine" - sexdeterrmine
#
files: files:
- path: "output/sexdeterrmine/test.bam" - path: output/samtools/test.tsv
md5sum: e667c7caad0bc4b7ac383fd023c654fc md5sum: c894abd0c78ea7760e0b54bbafb93722
- path: output/samtools/versions.yml
md5sum: dbd04b700335c8ad236bd667254c8dd8
- path: output/sexdeterrmine/sexdeterrmine.json
md5sum: 16d9e7891d4c92bc1d66db2e70e9d86f
- path: output/sexdeterrmine/test_sexdet.tsv
md5sum: 7ffc35e478de66939819a9ca4a5df2d7
- path: output/sexdeterrmine/versions.yml - path: output/sexdeterrmine/versions.yml
md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b md5sum: 077361101e8e7997aec3da8a01e59eee