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Update test file imports

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This commit is contained in:
Phil Ewels 2020-07-11 14:33:12 +02:00
parent a6b2485dab
commit d3f3432451
11 changed files with 10 additions and 15 deletions
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2
software/bwa/index/test/main.nf
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@ -1,6 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params) include '../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params) include '../main.nf' params(params)
// Define input channels // Define input channels

2
software/bwa/mem/test/main.nf
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@ -1,6 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include '../../../../nf-core/module_testing/check_process_outputs.nf' params(params) include '../../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params) include '../main.nf' params(params)
reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz' reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'

2
software/fastq_screen/test/main.nf
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@ -12,7 +12,7 @@ if (params.verbose){
println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args) println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args)
} }
// TODO: include '../../../nf-core/module_testing/check_process_outputs.nf' // TODO: include '../../../tests/functions/check_process_outputs.nf'
include '../main.nf' include '../main.nf'
// Define input channels // Define input channels

2
software/fastqc/test/main.nf
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@ -6,7 +6,7 @@ params.fastqc_args = ''
params.verbose = false params.verbose = false
// TODO: check the output files in some way // TODO: check the output files in some way
// include '../../../nf-core/module_testing/check_process_outputs.nf' // include '../../../tests/functions/check_process_outputs.nf'
include '../main.nf' include '../main.nf'
// Define input channels // Define input channels

2
software/gatk/dict/test/main.nf
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@ -1,6 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params) include '../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params) include '../main.nf' params(params)
// Define input channels // Define input channels

2
software/htslib/tabix/test/main.nf
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@ -1,6 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params) include '../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params) include '../main.nf' params(params)
// Define input channels // Define input channels

2
software/multiqc/test/main.nf
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@ -5,7 +5,7 @@ params.outdir = "."
params.verbose = false params.verbose = false
params.multiqc_args = '' params.multiqc_args = ''
// include '../../../nf-core/module_testing/check_process_outputs.nf' // include '../../../tests/functions/check_process_outputs.nf'
include '../main.nf' include '../main.nf'
if (params.verbose){ if (params.verbose){

2
software/samtools/faidx/test/main.nf
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@ -1,6 +1,6 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params) include '../../../tests/functions/check_process_outputs.nf' params(params)
include '../main.nf' params(params) include '../main.nf' params(params)
// Define input channels // Define input channels

7
software/tcoffee/test/main.nf
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@ -2,7 +2,7 @@
nextflow.preview.dsl = 2 nextflow.preview.dsl = 2
include check_output from '../../../nf-core/module_testing/check_process_outputs.nf' include check_output from '../../../tests/functions/check_process_outputs.nf'
include tcoffee from '../main.nf' include tcoffee from '../main.nf'
// Define input channels // Define input channels
@ -13,8 +13,3 @@ workflow {
tcoffee(fasta) tcoffee(fasta)
// .check_output() // .check_output()
} }

2
software/trim_galore/test/main.nf
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@ -12,7 +12,7 @@ if (params.verbose){
} }
// TODO: check the output files in some way // TODO: check the output files in some way
// include '../../../nf-core/module_testing/check_process_outputs.nf' // include '../../../tests/functions/check_process_outputs.nf'
include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters include '../main.nf' // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
ch_read_files = Channel ch_read_files = Channel

0
tests/check_process_outputs.nf → tests/functions/check_process_outputs.nf
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