Added profile for CI

nf-core · Oct 8, 2024 · 28032c6 · 28032c6
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commit 28032c6
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Showing 10 changed files with 14 additions and 36 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -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
 

diff --git a/conf/ci.config b/conf/ci.config
@@ -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"
+}
diff --git a/conf/test_contamination.config b/conf/test_contamination.config
@@ -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'

diff --git a/conf/test_contamination_tech_reps.config b/conf/test_contamination_tech_reps.config
@@ -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'
 

diff --git a/conf/test_mirgenedb.config b/conf/test_mirgenedb.config
@@ -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'

diff --git a/conf/test_nextflex.config b/conf/test_nextflex.config
@@ -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'

diff --git a/conf/test_skipfastp.config b/conf/test_skipfastp.config
@@ -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'

diff --git a/conf/test_technical_repeats.config b/conf/test_technical_repeats.config
@@ -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'

diff --git a/conf/test_umi.config b/conf/test_umi.config
@@ -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'

diff --git a/nextflow.config b/nextflow.config
@@ -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