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fix minor errors

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This commit is contained in:
Ramprasad Neethiraj 2022-05-03 15:04:37 +02:00
parent be085c0173
commit 26311aba2a
3 changed files with 5 additions and 1 deletions
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2
modules/cnvpytor/callcnvs/main.nf
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@ -19,7 +19,7 @@ process CNVPYTOR_CALLCNVS {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '1000' def bins = bin_sizes ?: '1000'
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
cnvpytor \\ cnvpytor \\

3
modules/cnvpytor/view/meta.yml
View file

@ -24,6 +24,9 @@ input:
- bin_sizes: - bin_sizes:
type: string type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000" description: list of binsizes separated by space e.g. "1000 10000" and "1000"
- output_format:
type: string
description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"
output: output:
- meta: - meta:

1
tests/modules/cnvpytor/view/test.yml
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@ -5,6 +5,7 @@
- cnvpytor/view - cnvpytor/view
files: files:
- path: output/cnvpytor/test_10000.vcf - path: output/cnvpytor/test_10000.vcf
- path: output/cnvpytor/test_100000.vcf
- path: output/cnvpytor/versions.yml - path: output/cnvpytor/versions.yml
- name: cnvpytor view test_cnvpytor_view tsv - name: cnvpytor view test_cnvpytor_view tsv