diff --git a/conf/test_full.config b/conf/test_full.config deleted file mode 100644 index 5826280..0000000 --- a/conf/test_full.config +++ /dev/null @@ -1,24 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running full-size tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a full size pipeline test. - - Use as follows: - nextflow run nf-core/deepmodeloptim -profile test_full, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'Full test profile' - config_profile_description = 'Full test dataset to check pipeline function' - - // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' - - // Fasta references - fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' -} diff --git a/conf/test_learn.config b/conf/test_learn.config deleted file mode 100644 index 31f7217..0000000 --- a/conf/test_learn.config +++ /dev/null @@ -1,43 +0,0 @@ -// for now it needs either crg config or local config to be given by the user -// TODO make this config stand alone. No need for other configs. - -params { - - config_profile_name = 'Test Learn profile' - config_profile_description = 'Minimal test dataset to check if a model that should learn actually does' - - // Input data - csv = "${projectDir}/bin/tests/test_data/titanic/titanic_stimulus.csv" - exp_conf = "${projectDir}/bin/tests/test_data/titanic/titanic_stimulus.json" // TODO make the data transformations available to titanic data types - model = "${projectDir}/bin/tests/test_model/titanic_model.py" - tune_conf = "${projectDir}/bin/tests/test_model/titanic_model_cpu.yaml" - -} - -// Limit resources so that this can run on GitHub Actions -process { - resourceLimits = [ - cpus: 2, - memory: 8.GB, - time: 6.h - ] - - maxRetries = params.max_retries - errorStrategy = params.err_start - - withLabel:process_low { - cpus = { 1 } - memory = { 4.GB * task.attempt } - time = { 10.m * task.attempt } - } - withLabel:process_medium{ - cpus = { 2 } - memory = { 6.GB * task.attempt } - time = { 30.m * task.attempt } - } - withLabel:process_high { - cpus = { 4 } - memory = { 8.GB * task.attempt } - time = { 1.h * task.attempt } - } -} diff --git a/conf/test_stub.config b/conf/test_stub.config index 861f494..482c7d1 100644 --- a/conf/test_stub.config +++ b/conf/test_stub.config @@ -8,10 +8,11 @@ params { config_profile_description = 'stub run to check pipeline function' // Input data - csv = "${projectDir}/bin/tests/test_data/dna_experiment/test.csv" - exp_conf = "${projectDir}/examples/test.json" - model = "${projectDir}/bin/tests/test_model/dnatofloat_model.py" - tune_conf = "${projectDir}/bin/tests/test_model/dnatofloat_model_cpu.yaml" + data = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/deepmodeloptim/testdata/titanic/titanic_stimulus.csv" + data_config = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/deepmodeloptim/testdata/titanic/titanic.yaml" + model = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/deepmodeloptim/testdata/titanic/titanic_model.py" + model_config = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/deepmodeloptim/testdata/titanic/titanic_model_cpu.yaml" + } process { @@ -21,8 +22,5 @@ process { memory: 6.GB, time: 6.h ] - - withName: 'INTERPRET_JSON|STIMULUS_NOISE_CSV|STIMULUS_SHUFFLE_CSV|STIMULUS_SPLIT_CSV|TORCH_TRAIN' { - container = 'quay.io/biocontainers/gawk:5.1.0' - } + container = 'quay.io/biocontainers/gawk:5.1.0' } diff --git a/nextflow.config b/nextflow.config index d9a105a..fe78f37 100644 --- a/nextflow.config +++ b/nextflow.config @@ -175,10 +175,8 @@ profiles { executor.memory = 8.GB } test { includeConfig "conf/test.config" } - test_learn { includeConfig "conf/test_learn.config" } test_stub { includeConfig "conf/test_stub.config" } local { includeConfig "conf/local.config" } - test_full { includeConfig 'conf/test_full.config' } } // Load nf-core custom profiles from different Institutions