From 28032c6040b7eddb27292ef03cb4c563dc8c61cd Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 8 Oct 2024 20:35:22 +0000 Subject: [PATCH] Added profile for CI --- .github/workflows/ci.yml | 2 +- conf/ci.config | 12 ++++++++++++ conf/test_contamination.config | 5 ----- conf/test_contamination_tech_reps.config | 5 ----- conf/test_mirgenedb.config | 5 ----- conf/test_nextflex.config | 5 ----- conf/test_skipfastp.config | 5 ----- conf/test_technical_repeats.config | 5 ----- conf/test_umi.config | 5 ----- nextflow.config | 1 + 10 files changed, 14 insertions(+), 36 deletions(-) create mode 100644 conf/ci.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 04a5af54..c62fc55a 100644 --- 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 new file mode 100644 index 00000000..9836bda3 --- /dev/null +++ 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 index 5e089656..266c288c 100644 --- 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 index f164bde4..5daf339c 100644 --- 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 index 9567dad4..097c73fe 100644 --- 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 index 17f1b721..465952f5 100644 --- 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 index 01216039..de786332 100644 --- 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 index 2c75e9bc..2c969ddd 100644 --- 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 index 16bc7256..5945efcf 100644 --- 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 index 0a686e9b..8fbc080d 100644 --- 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