From e40892c7075092183671f2e0fc8a8d4eb87eda12 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 14 Sep 2021 15:24:23 +0200 Subject: [PATCH] Align test_tsv to test --- .github/workflows/ci.yml | 68 ++++++++++---------- CHANGELOG.md | 1 + README.md | 2 +- conf/test.config | 7 +- conf/{test_tsv.config => test_direct.config} | 7 +- docs/usage.md | 2 +- nextflow.config | 4 +- 7 files changed, 46 insertions(+), 45 deletions(-) rename conf/{test_tsv.config => test_direct.config} (76%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7c7592fd0..9ad407e8b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -62,91 +62,91 @@ jobs: if [[ $NXF_VER = '' ]]; then sleep 1200; fi - name: BASIC Run the basic pipeline with directly supplied single-end FASTQ run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end + nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end - name: BASIC Run the basic pipeline with directly supplied paired-end FASTQ run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz' + nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz' - name: BASIC Run the basic pipeline with supplied --input BAM run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end + nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end - name: BASIC Run the basic pipeline with the test profile with, PE/SE, bwa aln run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --save_reference + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --save_reference - name: REFERENCE Basic workflow, with supplied indices run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' - name: REFERENCE Run the basic pipeline with FastA reference with `fna` extension run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker - name: REFERENCE Test with zipped reference input run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz' - name: FASTP Test fastp complexity filtering run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --complexity_filter_poly_g + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --complexity_filter_poly_g - name: ADAPTERREMOVAL Test skip paired end collapsing run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --skip_collapse + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_collapse - name: ADAPTERREMOVAL Test paired end collapsing but no trimming run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_pretrim,docker --skip_trim - name: ADAPTERREMOVAL Run the basic pipeline with paired end data without adapterRemoval run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --skip_adapterremoval + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_adapterremoval - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end option run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preserve5p + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p - name: ADAPTERREMOVAL Run the basic pipeline with merged only option run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mergedonly + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mergedonly - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end and merged reads only options run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preserve5p --mergedonly + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p --mergedonly - name: ADAPTER LIST Run the basic pipeline using an adapter list run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' - name: ADAPTER LIST Run the basic pipeline using an adapter list, skipping adapter removal run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval - name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_post_ar_trimming + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming - name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming, but skip adapterremoval run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_post_ar_trimming --skip_adapterremoval + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming --skip_adapterremoval - name: MAPPER_CIRCULARMAPPER Test running with CircularMapper run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2' - name: MAPPER_BWAMEM Test running with BWA Mem run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bwamem' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem' - name: MAPPER_BT2 Test running with BowTie2 run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1 + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1 - name: HOST_REMOVAL_FASTQ Run the basic pipeline with output unmapped reads as fastq run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --hostremoval_input_fastq - name: BAM_FILTERING Run basic mapping pipeline with mapping quality filtering, and unmapped export run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_unmapped_type 'fastq' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_unmapped_type 'fastq' - name: BAM_FILTERING Run basic mapping pipeline with post-mapping length filtering run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50 + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50 - name: PRESEQ Run basic mapping pipeline with different preseq mode run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10 + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10 - name: DEDUPLICATION Test with dedup run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --dedupper 'dedup' --dedup_all_merged + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --dedupper 'dedup' --dedup_all_merged - name: BEDTOOLS Test bedtools feature annotation run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3' - name: GENOTYPING_HC Test running GATK HaplotypeCaller run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION' - name: GENOTYPING_FB Test running FreeBayes run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes' - name: GENOTYPING_PC Test running pileupCaller run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'pileupcaller' @@ -155,25 +155,25 @@ jobs: nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'angsd' - name: GENOTYPING_BCFTOOLS Test running FreeBayes with bcftools stats turned on run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes' - name: TRIMBAM Test bamutils works alone run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_trim_bam + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_trim_bam - name: PMDTOOLS Test PMDtools works alone run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_pmdtools - name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies - name: COMPLEX LANE/LIBRARY MERGING Test running lane and library merging prior to GATK UnifiedGenotyper and running MultiVCFAnalyzer run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer - name: GENOTYPING_UG ON TRIMMED BAM Test run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval @@ -187,17 +187,17 @@ jobs: for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P databases/malt/; done - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output - name: METAGENOMIC Run the basic pipeline but low-complexity filtered reads going into MALT run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter - name: MALTEXTRACT Download resource files run: | mkdir -p databases/maltextract for i in ncbi.tre ncbi.map; do wget https://github.com/rhuebler/HOPS/raw/0.33/Resources/"$i" -P databases/maltextract/; done - name: MALTEXTRACT Basic with MALT plus MaltExtract run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into Kraken run: | nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_kraken,docker --run_bam_filtering --bam_unmapped_type 'fastq' @@ -212,4 +212,4 @@ jobs: nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio - name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled' \ No newline at end of file + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled' \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index ed4329b32..bf8c396b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files. - [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them - [#792](https://github.com/nf-core/eager/issues/792) Fixed java error messages for AdapterRemovalFixPrefix being hidden in output +- [#794](https://github.com/nf-core/eager/issues/794) Aligned default test profile with nf-core standards (`test_tsv` is now `test`) ### `Dependencies` diff --git a/README.md b/README.md index 479d2eae8..284f9046d 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool 3. Download the pipeline and test it on a minimal dataset with a single command: ```bash - nextflow run nf-core/eager -profile test_tsv, + nextflow run nf-core/eager -profile test, ``` > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. diff --git a/conf/test.config b/conf/test.config index 9cffc92f5..bce379d44 100644 --- a/conf/test.config +++ b/conf/test.config @@ -4,12 +4,11 @@ * ------------------------------------------------- * Defines bundled input files and everything required * to run a fast and simple test. Use as follows: - * nextflow run nf-core/eager -profile test, + * nextflow run nf-core/eager -profile test, docker (or singularity, or conda) */ includeConfig 'test_resources.config' - params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -19,9 +18,7 @@ params { max_time = 48.h genome = false //Input data - single_end = false + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_fastq.tsv' // Genome references fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta' - // Ignore `--input` as otherwise the parameter validation will throw an error - schema_ignore_params = 'genomes,input_paths,input' } diff --git a/conf/test_tsv.config b/conf/test_direct.config similarity index 76% rename from conf/test_tsv.config rename to conf/test_direct.config index bce379d44..9cffc92f5 100644 --- a/conf/test_tsv.config +++ b/conf/test_direct.config @@ -4,11 +4,12 @@ * ------------------------------------------------- * Defines bundled input files and everything required * to run a fast and simple test. Use as follows: - * nextflow run nf-core/eager -profile test, docker (or singularity, or conda) + * nextflow run nf-core/eager -profile test, */ includeConfig 'test_resources.config' + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -18,7 +19,9 @@ params { max_time = 48.h genome = false //Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_fastq.tsv' + single_end = false // Genome references fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta' + // Ignore `--input` as otherwise the parameter validation will throw an error + schema_ignore_params = 'genomes,input_paths,input' } diff --git a/docs/usage.md b/docs/usage.md index 4c2f5f77a..ad427be05 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -111,7 +111,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. * A generic configuration profile to be used with [Conda](https://conda.io/docs/) * Pulls most software from [Bioconda](https://bioconda.github.io/) -* `test_tsv` +* `test` * A profile with a complete configuration for automated testing * Includes links to test data so needs no other parameters diff --git a/nextflow.config b/nextflow.config index a9f324245..a1952c731 100644 --- a/nextflow.config +++ b/nextflow.config @@ -348,14 +348,14 @@ profiles { shifter.enabled = false charliecloud.enabled = true } - test { includeConfig 'conf/test.config' } + test { includeConfig 'conf/test.config'} + test_direct { includeConfig 'conf/test_direct.config' } test_full { includeConfig 'conf/test_full.config' } test_bam { includeConfig 'conf/test_bam.config'} test_fna { includeConfig 'conf/test_fna.config'} test_humanbam { includeConfig 'conf/test_humanbam.config' } test_pretrim { includeConfig 'conf/test_pretrim.config' } test_kraken { includeConfig 'conf/test_kraken.config' } - test_tsv { includeConfig 'conf/test_tsv.config'} test_tsv_bam { includeConfig 'conf/test_tsv_bam.config'} test_tsv_fna { includeConfig 'conf/test_tsv_fna.config'} test_tsv_humanbam { includeConfig 'conf/test_tsv_humanbam.config' }