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Added profile for CI
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nschcolnicov committed Oct 8, 2024
1 parent 314524a commit 28032c6
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Showing 10 changed files with 14 additions and 36 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -70,7 +70,7 @@ jobs:
--ci \
--shard ${{ matrix.shard }}/${{ env.SHARDS }} \
--changed-since HEAD^ \
--profile "+${{ matrix.profile }}" \
--profile "+${{ matrix.profile }},ci_test" \
--filter pipeline \
--junitxml=test.xml
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12 changes: 12 additions & 0 deletions conf/ci.config
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@@ -0,0 +1,12 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for setting resources in CI
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
----------------------------------------------------------------------------------------
*/

//max_cpu, max_ram and max_time was removed, setting all process to the process_low label to allow for running in CI
process {
label = "process_low"
}
5 changes: 0 additions & 5 deletions conf/test_contamination.config
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Expand Up @@ -14,11 +14,6 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function with contamination filter'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data

input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
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5 changes: 0 additions & 5 deletions conf/test_contamination_tech_reps.config
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Expand Up @@ -15,11 +15,6 @@ params {
config_profile_name = 'Test technical repeats profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats_short.csv'

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5 changes: 0 additions & 5 deletions conf/test_mirgenedb.config
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Expand Up @@ -14,11 +14,6 @@ params {
config_profile_name = 'Test profile with mirgeneDB inputs and run mirdeep2'
config_profile_description = 'Minimal test dataset to check pipeline function with mirgeneDB inputs and run mirdeep2'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_test_short.csv'
fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
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5 changes: 0 additions & 5 deletions conf/test_nextflex.config
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Expand Up @@ -15,11 +15,6 @@ params {
config_profile_name = 'Nextflex Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/smrnaseq/samplesheet/v2.0/samplesheet_test_nextflex.csv'
mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa'
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5 changes: 0 additions & 5 deletions conf/test_skipfastp.config
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Expand Up @@ -15,11 +15,6 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function skipping trimming'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data

input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_skipfastp.csv'
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5 changes: 0 additions & 5 deletions conf/test_technical_repeats.config
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Expand Up @@ -14,11 +14,6 @@ params {
config_profile_name = 'Test technical repeats profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data

input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats.csv'
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5 changes: 0 additions & 5 deletions conf/test_umi.config
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Expand Up @@ -14,11 +14,6 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data

input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_umi.csv'
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -220,6 +220,7 @@ profiles {
test_contamination_tech_reps { includeConfig 'conf/test_contamination_tech_reps.config' }
test_skipfastp { includeConfig 'conf/test_skipfastp.config' }
test_nextflex { includeConfig 'conf/test_nextflex.config' }
ci_test { includeConfig 'conf/ci.config' }


//Protocol specific profiles
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