diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c47e8cdc..6c95a2b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -36,7 +36,7 @@ jobs: - "test_motus" - "test_falco" - "test_fastp" - - "test_adapterremoval" + - "test_alternativepreprocessing" - "test_bbduk" - "test_prinseqplusplus" diff --git a/conf/test.config b/conf/test.config index 0c6d260d..4e457585 100644 --- a/conf/test.config +++ b/conf/test.config @@ -11,17 +11,17 @@ */ params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + 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' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' perform_shortread_qc = true perform_shortread_redundancyestimation = true perform_longread_qc = true diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config deleted file mode 100644 index f6b2c727..00000000 --- a/conf/test_adapterremoval.config +++ /dev/null @@ -1,54 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 for adapterremoval' - config_profile_description = "Minimal test to check the alternative short-read QC function, adapterremoval" - - // 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 + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = true - perform_longread_qc = true - shortread_qc_tool = 'adapterremoval' - perform_shortread_complexityfilter = true - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - perform_runmerging = true - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = true - run_kraken2 = true - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_ganon = false - run_kmcp = false -} - -process { - withName: MALT_RUN { - maxForks = 1 - ext.args = { "-m ${params.malt_mode} -J-Xmx12G" } - } - withName: NONPAREIL_NONPAREIL { - ext.args = { "-k 5" } - } -} diff --git a/conf/test_alternativepreprocessing.config b/conf/test_alternativepreprocessing.config new file mode 100644 index 00000000..4655c3a3 --- /dev/null +++ b/conf/test_alternativepreprocessing.config @@ -0,0 +1,56 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 for adapterremoval' + config_profile_description = "Minimal test to check the alternative short-read QC function, adapterremoval" + + // 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 + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = true + perform_longread_qc = true + shortread_qc_tool = 'adapterremoval' + longread_adapterremoval_tool = 'porechop' + longread_filter_tool = 'filtlong' + perform_shortread_complexityfilter = true + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + perform_runmerging = true + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = true + run_kraken2 = true + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_ganon = false + run_kmcp = false +} + +process { + withName: MALT_RUN { + maxForks = 1 + ext.args = { "-m ${params.malt_mode} -J-Xmx12G" } + } + withName: NONPAREIL_NONPAREIL { + ext.args = { "-k 5" } + } +} diff --git a/conf/test_bbduk.config b/conf/test_bbduk.config index 6bb39510..58128613 100644 --- a/conf/test_bbduk.config +++ b/conf/test_bbduk.config @@ -11,36 +11,36 @@ */ params { - config_profile_name = 'Test profile for bbduk' - config_profile_description = "Minimal test to check the default tool of short-read complexity filtering, bbduk" + config_profile_name = 'Test profile for bbduk' + config_profile_description = "Minimal test to check the default tool of short-read complexity filtering, bbduk" // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = true - perform_longread_qc = true - perform_shortread_complexityfilter = true - shortread_complexityfilter_tool = 'bbduk' - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - perform_runmerging = true - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = true - run_kraken2 = true - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_ganon = false - run_kmcp = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = true + perform_longread_qc = true + perform_shortread_complexityfilter = true + shortread_complexityfilter_tool = 'bbduk' + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + perform_runmerging = true + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = true + run_kraken2 = true + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_ganon = false + run_kmcp = false } process { diff --git a/conf/test_falco.config b/conf/test_falco.config index 8e22cde1..2e1f626d 100644 --- a/conf/test_falco.config +++ b/conf/test_falco.config @@ -11,36 +11,36 @@ */ params { - config_profile_name = 'Test profile for Falco' - config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function but running falco instead of fastqc. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others" + config_profile_name = 'Test profile for Falco' + config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function but running falco instead of fastqc. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others" // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - preprocessing_qc_tool = 'falco' - perform_shortread_qc = true - perform_longread_qc = true - perform_shortread_complexityfilter = false - perform_shortread_hostremoval = false - perform_longread_hostremoval = false - perform_runmerging = false - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = false - run_kraken2 = false - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_ganon = false - run_kmcp = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + preprocessing_qc_tool = 'falco' + perform_shortread_qc = true + perform_longread_qc = true + perform_shortread_complexityfilter = false + perform_shortread_hostremoval = false + perform_longread_hostremoval = false + perform_runmerging = false + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = false + run_kraken2 = false + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_ganon = false + run_kmcp = false } process { diff --git a/conf/test_fastp.config b/conf/test_fastp.config index 48daab96..54c82250 100644 --- a/conf/test_fastp.config +++ b/conf/test_fastp.config @@ -11,38 +11,38 @@ */ params { - config_profile_name = 'Test profile for fastp' - config_profile_description = "Minimal test to check the default short-read QC function, fastp" + config_profile_name = 'Test profile for fastp' + config_profile_description = "Minimal test to check the default short-read QC function, fastp" // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = true - perform_longread_qc = true - shortread_qc_tool = 'fastp' - perform_shortread_redundancyestimation = true - perform_shortread_complexityfilter = true - shortread_complexityfilter_tool = 'fastp' - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - perform_runmerging = true - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = true - run_kraken2 = true - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_ganon = false - run_kmcp = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = true + perform_longread_qc = true + shortread_qc_tool = 'fastp' + perform_shortread_redundancyestimation = true + perform_shortread_complexityfilter = true + shortread_complexityfilter_tool = 'fastp' + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + perform_runmerging = true + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = true + run_kraken2 = true + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_ganon = false + run_kmcp = false } process { diff --git a/conf/test_full.config b/conf/test_full.config index 91cb08c7..691928fd 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -9,15 +9,15 @@ */ params { - config_profile_name = 'Full test profile' - config_profile_description = 'Full test dataset to check pipeline function' + config_profile_name = 'Full test profile' + config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_full.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v1.1.csv' + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_full.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v1.2.csv' // Genome references - hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz' + hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz' save_preprocessed_reads = false diff --git a/conf/test_malt.config b/conf/test_malt.config index 496306b9..a20ae546 100644 --- a/conf/test_malt.config +++ b/conf/test_malt.config @@ -15,36 +15,36 @@ // params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test to check malt function' + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test to check malt function' // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_malt.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = false - perform_longread_qc = false - perform_shortread_redundancyestimation = false - perform_shortread_complexityfilter = false - perform_shortread_hostremoval = false - perform_longread_hostremoval = false - perform_runmerging = false - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = false - run_kraken2 = false - run_bracken = false - run_malt = true - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_ganon = false - run_kmcp = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_malt.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = false + perform_longread_qc = false + perform_shortread_redundancyestimation = false + perform_shortread_complexityfilter = false + perform_shortread_hostremoval = false + perform_longread_hostremoval = false + perform_runmerging = false + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = false + run_kraken2 = false + run_bracken = false + run_malt = true + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_ganon = false + run_kmcp = false } process { diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config index 267cd533..cad2e85e 100644 --- a/conf/test_nopreprocessing.config +++ b/conf/test_nopreprocessing.config @@ -11,37 +11,38 @@ */ params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function' + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test dataset skipping all preprocessing 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' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = false - perform_longread_qc = false - perform_shortread_redundancyestimation = false - perform_shortread_complexityfilter = false - perform_shortread_hostremoval = false - perform_longread_hostremoval = false - perform_runmerging = false - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = true - run_kraken2 = true - run_bracken = true - run_malt = false // too big with other profiles on GHA - run_metaphlan = true - run_centrifuge = true - run_diamond = true - run_krakenuniq = true - run_motus = false - run_kmcp = true - run_ganon = true - run_krona = true + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = false + perform_longread_qc = false + perform_shortread_redundancyestimation = false + perform_shortread_complexityfilter = false + perform_shortread_hostremoval = false + perform_longread_hostremoval = false + perform_runmerging = false + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = true + run_kraken2 = true + run_bracken = true + run_malt = false + // too big with other profiles on GHA + run_metaphlan = true + run_centrifuge = true + run_diamond = true + run_krakenuniq = true + run_motus = false + run_kmcp = true + run_ganon = true + run_krona = true } process { diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config index 36f2c3f9..ebf3a22c 100644 --- a/conf/test_noprofiling.config +++ b/conf/test_noprofiling.config @@ -11,37 +11,37 @@ */ params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function' + 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' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = true - perform_longread_qc = true - perform_shortread_redundancyestimation = true - shortread_qc_mergepairs = true - perform_shortread_complexityfilter = true - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - perform_runmerging = true - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = false - run_kraken2 = false - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_kmcp = false - run_ganon = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = true + perform_longread_qc = true + perform_shortread_redundancyestimation = true + shortread_qc_mergepairs = true + perform_shortread_complexityfilter = true + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + perform_runmerging = true + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = false + run_kraken2 = false + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_kmcp = false + run_ganon = false } process { diff --git a/conf/test_nothing.config b/conf/test_nothing.config index 767bf943..8f339100 100644 --- a/conf/test_nothing.config +++ b/conf/test_nothing.config @@ -11,36 +11,36 @@ */ params { - config_profile_name = 'Test profile' - config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others" + config_profile_name = 'Test profile' + config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others" // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = false - perform_longread_qc = false - perform_shortread_redundancyestimation = false - perform_shortread_complexityfilter = false - perform_shortread_hostremoval = false - perform_longread_hostremoval = false - perform_runmerging = false - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = false - run_kraken2 = false - run_bracken = false - run_malt = false - run_metaphlan = false - run_centrifuge = false - run_diamond = false - run_krakenuniq = false - run_motus = false - run_kmcp = false - run_ganon = false + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' + perform_shortread_qc = false + perform_longread_qc = false + perform_shortread_redundancyestimation = false + perform_shortread_complexityfilter = false + perform_shortread_hostremoval = false + perform_longread_hostremoval = false + perform_runmerging = false + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = false + run_kraken2 = false + run_bracken = false + run_malt = false + run_metaphlan = false + run_centrifuge = false + run_diamond = false + run_krakenuniq = false + run_motus = false + run_kmcp = false + run_ganon = false } process { diff --git a/conf/test_prinseqplusplus.config b/conf/test_prinseqplusplus.config index 147d37cf..d974d344 100644 --- a/conf/test_prinseqplusplus.config +++ b/conf/test_prinseqplusplus.config @@ -11,17 +11,17 @@ */ params { - config_profile_name = 'Test profile for prinseqplusplus' - config_profile_description = "Minimal test to check the alternative tool of short-read complexity filtering, prinseqplusplus" + config_profile_name = 'Test profile for prinseqplusplus' + config_profile_description = "Minimal test to check the alternative tool of short-read complexity filtering, prinseqplusplus" // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' // Input data input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv' perform_shortread_qc = true perform_longread_qc = true perform_shortread_redundancyestimation = false diff --git a/nextflow.config b/nextflow.config index 0d7a423f..9d4ff993 100644 --- a/nextflow.config +++ b/nextflow.config @@ -324,7 +324,7 @@ profiles { test_malt { includeConfig 'conf/test_malt.config' } test_falco { includeConfig 'conf/test_falco.config' } test_fastp { includeConfig 'conf/test_fastp.config' } - test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' } + test_alternativepreprocessing { includeConfig 'conf/test_alternativepreprocessing.config' } test_bbduk { includeConfig 'conf/test_bbduk.config' } test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.config' }