diff --git a/conf/test_screening.config b/conf/test_screening.config index a359596..6731a61 100644 --- a/conf/test_screening.config +++ b/conf/test_screening.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Test screening 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 = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test.csv" analysis = 'screening' @@ -37,4 +32,9 @@ process { withName: BAGEL2_BF { ext.args = '-s 3' // Seed to avoid random errors due to a too small sample } + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] } diff --git a/conf/test_screening_count_table.config b/conf/test_screening_count_table.config index 9dfefe9..8e8e2be 100644 --- a/conf/test_screening_count_table.config +++ b/conf/test_screening_count_table.config @@ -9,16 +9,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test screening profile with an input count table' 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 count_table = params.pipelines_testdata_base_path + "crisprseq/testdata/count_table.tsv" analysis = 'screening' diff --git a/conf/test_screening_paired.config b/conf/test_screening_paired.config index 1115f2a..0a9eb66 100644 --- a/conf/test_screening_paired.config +++ b/conf/test_screening_paired.config @@ -14,10 +14,6 @@ params { config_profile_name = 'Test screening profile paired-end' config_profile_description = 'Minimal test dataset to check pipeline function for paired-end data' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' // Input data input = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test_paired.csv" @@ -29,4 +25,9 @@ process { withName: BAGEL2_BF { ext.args = '-s 3' // Seed to avoid random errors due to a too small sample } + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] } diff --git a/conf/test_screening_rra.config b/conf/test_screening_rra.config index ce9c94b..a82addf 100644 --- a/conf/test_screening_rra.config +++ b/conf/test_screening_rra.config @@ -14,10 +14,6 @@ params { config_profile_name = 'Test screening 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 = params.pipelines_testdata_base_path + "crisprseq/testdata/samplesheet_test.csv" @@ -34,4 +30,9 @@ process { withName: BAGEL2_BF { ext.args = '-s 3' // Seed to avoid random errors due to a too small sample } + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] } diff --git a/conf/test_umis.config b/conf/test_umis.config index d77b71f..a9da431 100644 --- a/conf/test_umis.config +++ b/conf/test_umis.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Test profile UMIs' config_profile_description = 'Minimal test dataset to check pipeline function with UMIs option' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = params.pipelines_testdata_base_path + "crisprseq/testdata-edition/samplesheet_test_umis.csv" analysis = 'targeted' @@ -27,3 +22,11 @@ params { // Aligner aligner = 'minimap2' } + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +}