diff --git a/conf/test_nothing.config b/conf/test_nothing.config new file mode 100644 index 0000000..e4846a3 --- /dev/null +++ b/conf/test_nothing.config @@ -0,0 +1,47 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/taxprofiler -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test dataset without performing any profiling 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 + // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets + // TODO nf-core: Give any required params for the test so that command line flags are not needed + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' + databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' + perform_shortread_qc = false + perform_longread_qc = false + perform_shortread_complexityfilter = false + perform_shortread_hostremoval = false + perform_longread_hostremoval = false + perform_runmerging = false + hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = false + run_kraken2 = false + run_malt = false + run_metaphlan3 = false + run_centrifuge = false + run_diamond = false + run_motus = false +} + +process { + withName: MALT_RUN { + maxForks = 1 + } +} diff --git a/nextflow.config b/nextflow.config index 58c9254..4a83031 100644 --- a/nextflow.config +++ b/nextflow.config @@ -204,11 +204,12 @@ profiles { podman.enabled = false shifter.enabled = false } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - test_noprofiling { includeConfig 'conf/test_noprofiling.config' } - test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } - test_motus { includeConfig 'conf/test_motus.config' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + test_noprofiling { includeConfig 'conf/test_noprofiling.config' } + test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } + test_nothing { includeConfig 'conf/test_nothing.config' } + test_motus { includeConfig 'conf/test_motus.config' } } // Load igenomes.config if required