From d3f34324517635fda2c6f5a67146091209800720 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 11 Jul 2020 14:33:12 +0200 Subject: [PATCH] Update test file imports --- software/bwa/index/test/main.nf | 2 +- software/bwa/mem/test/main.nf | 2 +- software/fastq_screen/test/main.nf | 2 +- software/fastqc/test/main.nf | 2 +- software/gatk/dict/test/main.nf | 2 +- software/htslib/tabix/test/main.nf | 2 +- software/multiqc/test/main.nf | 2 +- software/samtools/faidx/test/main.nf | 2 +- software/tcoffee/test/main.nf | 7 +------ software/trim_galore/test/main.nf | 2 +- tests/{ => functions}/check_process_outputs.nf | 0 11 files changed, 10 insertions(+), 15 deletions(-) rename tests/{ => functions}/check_process_outputs.nf (100%) diff --git a/software/bwa/index/test/main.nf b/software/bwa/index/test/main.nf index 6acb4d61..8e36c9ac 100644 --- a/software/bwa/index/test/main.nf +++ b/software/bwa/index/test/main.nf @@ -1,6 +1,6 @@ #!/usr/bin/env nextflow 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) // Define input channels diff --git a/software/bwa/mem/test/main.nf b/software/bwa/mem/test/main.nf index 49ec1efc..3a609477 100644 --- a/software/bwa/mem/test/main.nf +++ b/software/bwa/mem/test/main.nf @@ -1,6 +1,6 @@ #!/usr/bin/env nextflow 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) reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz' diff --git a/software/fastq_screen/test/main.nf b/software/fastq_screen/test/main.nf index be2b486e..4365bf55 100755 --- a/software/fastq_screen/test/main.nf +++ b/software/fastq_screen/test/main.nf @@ -12,7 +12,7 @@ if (params.verbose){ 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' // Define input channels diff --git a/software/fastqc/test/main.nf b/software/fastqc/test/main.nf index 9ec2d338..a740dbe5 100755 --- a/software/fastqc/test/main.nf +++ b/software/fastqc/test/main.nf @@ -6,7 +6,7 @@ params.fastqc_args = '' params.verbose = false // 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' // Define input channels diff --git a/software/gatk/dict/test/main.nf b/software/gatk/dict/test/main.nf index 41c1862c..c1005d37 100644 --- a/software/gatk/dict/test/main.nf +++ b/software/gatk/dict/test/main.nf @@ -1,6 +1,6 @@ #!/usr/bin/env nextflow 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) // Define input channels diff --git a/software/htslib/tabix/test/main.nf b/software/htslib/tabix/test/main.nf index 6fd80089..478d38f5 100644 --- a/software/htslib/tabix/test/main.nf +++ b/software/htslib/tabix/test/main.nf @@ -1,6 +1,6 @@ #!/usr/bin/env nextflow 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) // Define input channels diff --git a/software/multiqc/test/main.nf b/software/multiqc/test/main.nf index 6e630211..dbfc3c98 100755 --- a/software/multiqc/test/main.nf +++ b/software/multiqc/test/main.nf @@ -5,7 +5,7 @@ params.outdir = "." params.verbose = false params.multiqc_args = '' -// include '../../../nf-core/module_testing/check_process_outputs.nf' +// include '../../../tests/functions/check_process_outputs.nf' include '../main.nf' if (params.verbose){ diff --git a/software/samtools/faidx/test/main.nf b/software/samtools/faidx/test/main.nf index f01ab6c9..39ad118c 100644 --- a/software/samtools/faidx/test/main.nf +++ b/software/samtools/faidx/test/main.nf @@ -1,6 +1,6 @@ #!/usr/bin/env nextflow 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) // Define input channels diff --git a/software/tcoffee/test/main.nf b/software/tcoffee/test/main.nf index 92df03d2..26fd68f2 100644 --- a/software/tcoffee/test/main.nf +++ b/software/tcoffee/test/main.nf @@ -2,7 +2,7 @@ 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' // Define input channels @@ -13,8 +13,3 @@ workflow { tcoffee(fasta) // .check_output() } - - - - - diff --git a/software/trim_galore/test/main.nf b/software/trim_galore/test/main.nf index 7f49567f..5d1183a3 100755 --- a/software/trim_galore/test/main.nf +++ b/software/trim_galore/test/main.nf @@ -12,7 +12,7 @@ if (params.verbose){ } // 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 ch_read_files = Channel diff --git a/tests/check_process_outputs.nf b/tests/functions/check_process_outputs.nf similarity index 100% rename from tests/check_process_outputs.nf rename to tests/functions/check_process_outputs.nf