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updating paths in test.yml

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jvhagey 2022-05-24 16:27:00 -04:00
parent f1fc7fc38e
commit b8aaea7429
4 changed files with 16 additions and 15 deletions
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2
modules/gamma/gamma/main.nf
View file

@ -1,6 +1,6 @@
def VERSION = '2.1' // Version information not provided by tool on CLI def VERSION = '2.1' // Version information not provided by tool on CLI
process GAMMA { process GAMMA_GAMMA {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'

3
modules/gamma/gamma/meta.yml
View file

@ -1,4 +1,4 @@
name: "gamma" name: "gamma_gamma"
description: Gene Allele Mutation Microbial Assessment description: Gene Allele Mutation Microbial Assessment
keywords: keywords:
- gamma - gamma
@ -61,3 +61,4 @@ output:
authors: authors:
- "@sateeshperi" - "@sateeshperi"
- "@rastanton" - "@rastanton"
- "@jvhagey"

6
tests/modules/gamma/gamma/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { GAMMA } from '../../../../modules/gamma/gamma/main.nf' include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
workflow test_unzip { workflow test_unzip {
@ -13,7 +13,7 @@ workflow test_unzip {
db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ] db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
GAMMA ( input, db ) GAMMA_GAMMA ( input, db )
} }
workflow test_gamma { workflow test_gamma {
@ -25,5 +25,5 @@ workflow test_gamma {
db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
GAMMA ( input, db ) GAMMA_GAMMA ( input, db )
} }

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

@ -4,14 +4,14 @@
- gamma/gamma - gamma/gamma
- gamma - gamma
files: files:
- path: /tmp/tmppm1ybfln/gamma/test.fasta - path: output/gamma/gamma/test.fasta
md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
- path: /tmp/tmppm1ybfln/gamma/test.gamma - path: output/gamma/gamma/test.gamma
md5sum: 46165a89e10b7315d3a9b0aa6c561626 md5sum: 46165a89e10b7315d3a9b0aa6c561626
- path: /tmp/tmppm1ybfln/gamma/test.psl - path: output/gamma/gamma/test.psl
md5sum: f489ce4602ddbcb692d5781ee3fbf449 md5sum: f489ce4602ddbcb692d5781ee3fbf449
- path: /tmp/tmppm1ybfln/gamma/versions.yml - path: output/gamma/gamma/versions.yml
md5sum: ad23c3ec60663598543cbe8bc74bc4ab md5sum: 8baafec7b3b87f788f69e30d317c9722
- name: gamma gamma test_gamma - name: gamma gamma test_gamma
command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
@ -19,11 +19,11 @@
- gamma/gamma - gamma/gamma
- gamma - gamma
files: files:
- path: /tmp/tmpw3chm6da/gamma/test.fasta - path: output/gamma/gamma/test.fasta
md5sum: df37b48466181311e0a679f3c5878484 md5sum: df37b48466181311e0a679f3c5878484
- path: /tmp/tmpw3chm6da/gamma/test.gamma - path: output/gamma/gamma/test.gamma
md5sum: 3256708fa517a65ed01d99e0e3c762ae md5sum: 3256708fa517a65ed01d99e0e3c762ae
- path: /tmp/tmpw3chm6da/gamma/test.psl - path: output/gamma/gamma/test.psl
md5sum: 162a2757ed3b167ae1e0cdb24213f940 md5sum: 162a2757ed3b167ae1e0cdb24213f940
- path: /tmp/tmpw3chm6da/gamma/versions.yml - path: output/gamma/gamma/versions.yml
md5sum: 3fefb5b46c94993362243c5f9a472057 md5sum: b75c2871d8cac2f8ac67c0fbd22babd6