diff --git a/main.nf b/main.nf new file mode 100644 index 0000000..de12f61 --- /dev/null +++ b/main.nf @@ -0,0 +1,3 @@ +/* + * not actually used - just a placeholder + */ diff --git a/modules/UMCUGenetics/utils/EditSummaryFileHappy.nf b/modules/UMCUGenetics/utils/EditSummaryFileHappy.nf deleted file mode 100644 index 4a90842..0000000 --- a/modules/UMCUGenetics/utils/EditSummaryFileHappy.nf +++ /dev/null @@ -1,30 +0,0 @@ -process EditSummaryFileHappy { - tag "$meta.id" - label 'EditSummaryFileHappy' - shell = ['/bin/bash', '-euo', 'pipefail'] - - input: - // meta should have the keys 'id', 'query' and 'truth' - tuple val(meta), path(summary_csv) - - output: - path("*_INDEL_PASS.summary.csv"), emit: indel_pass_csv - path("*_INDEL_ALL.summary.csv"), emit: indel_all_csv - path("*_SNP_PASS.summary.csv"), emit: snp_pass_csv - path("*_SNP_ALL.summary.csv"), emit: snp_all_csv - - script: - """ - # Add samplenames as columns (header and row values) at start of line - sed '1s/^/samples,sample_truth,sample_query,/; 2,\$s/^/${meta.truth}_${meta.query},${meta.truth},${meta.query},/' ${summary_csv} > ${summary_csv}.tmp - - # Split file including header (first line) - awk -F',' 'FNR==1{hdr=\$0;next} { - print hdr>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv"; - print \$0>>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv" - }' ${summary_csv}.tmp - - # Remove tmp files - rm ${summary_csv}.tmp - """ -} diff --git a/modules/UMCUGenetics/utils/editsummaryfilehappy/main.nf b/modules/UMCUGenetics/utils/editsummaryfilehappy/main.nf new file mode 100644 index 0000000..1ae0a11 --- /dev/null +++ b/modules/UMCUGenetics/utils/editsummaryfilehappy/main.nf @@ -0,0 +1,41 @@ +process UTILS_EDITSUMMARYFILEHAPPY { + tag "${meta.id}" + label 'process_low' + + input: + tuple val(meta), path(summary_csv) + + output: + path("*_INDEL_PASS.summary.csv"), emit: indel_pass_csv + path("*_INDEL_ALL.summary.csv"), emit: indel_all_csv + path("*_SNP_PASS.summary.csv"), emit: snp_pass_csv + path("*_SNP_ALL.summary.csv"), emit: snp_all_csv + + when: + task.ext.when == null || task.ext.when + + script: + """ + # Add samplenames as columns (header and row values) at start of line + sed '1s/^/samples,sample_truth,sample_query,/; 2,\$s/^/${meta.truth}_${meta.query},${meta.truth},${meta.query},/' ${summary_csv} > ${summary_csv}.tmp + + # Split file including header (first line) + awk -F',' 'FNR==1{hdr=\$0;next} { + print hdr>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv"; + print \$0>>"${meta.truth}_${meta.query}_"\$4"_"\$5".summary.csv" + }' ${summary_csv}.tmp + + # Remove tmp files + rm ${summary_csv}.tmp + """ + + stub: + """ + touch ${meta.truth}_${meta.query}_INDEL_PASS.summary.csv + touch ${meta.truth}_${meta.query}_INDEL_ALL.summary.csv + touch ${meta.truth}_${meta.query}_SNP_PASS.summary.csv + touch ${meta.truth}_${meta.query}_SNP_ALL.summary.csv + """ + + +} diff --git a/modules/UMCUGenetics/utils/editsummaryfilehappy/meta.yml b/modules/UMCUGenetics/utils/editsummaryfilehappy/meta.yml new file mode 100644 index 0000000..d5c10a2 --- /dev/null +++ b/modules/UMCUGenetics/utils/editsummaryfilehappy/meta.yml @@ -0,0 +1,41 @@ +name: editsummaryfilehappy +description: Reformat the happy summary file for GIABEval +keywords: + - giab + - GIABEval + - utils + +tools: + - bash: + description: | + Util process, using only bash +input: + - - meta: + type: map + description: | + Groovy Map containing sample information it should have the keys [id: '', 'query', 'truth'] + - summary_csv: + type: file + description: summary output csv from happy +output: + indel_pass_csv: + - "*_INDEL_PASS.summary.csv": + type: file + description: "INDELs that pass the criteria" + indel_all_csv: + - "*_INDEL_ALL.summary.csv": + type: file + description: "All indels" + snp_pass_csv: + - "*_SNP_PASS.summary.csv": + type: file + description: "SNPs that pass the criteria" + snp_all_csv: + - "*_SNP_ALL.summary.csv": + type: file + description: "All SNPs" + +authors: + - "@ellendejong" + - "@melferink" + diff --git a/modules/UMCUGenetics/utils/editsummaryfilehappy/tests/main.nf.test b/modules/UMCUGenetics/utils/editsummaryfilehappy/tests/main.nf.test new file mode 100644 index 0000000..8962abd --- /dev/null +++ b/modules/UMCUGenetics/utils/editsummaryfilehappy/tests/main.nf.test @@ -0,0 +1,26 @@ +nextflow_process { + name "Test UTILS_EDITSUMMARYFILEHAPPY" + script "../main.nf" + process "UTILS_EDITSUMMARYFILEHAPPY" + + tag "modules" + tag "modules_umcugenetics" + tag "happy" + + test("stub") { + options "-stub" + when{ + process{ + """ + input[0] = [ + [id: 'test', truth: 'truthsample', query: "querysample"], // meta map + file("demo_summary.csv") + ] + """ + } + } + then { + assert process.success + } + } +} diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..609c4c9 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,14 @@ +config { + // location for all nf-tests + testsDir = "." + + // nf-test directory including temporary files for each test + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" + + // location of an optional nextflow.config file specific for executing tests + configFile = "tests/config/nf-test.config" + + // run all test with the defined docker profile from the main nextflow.config + profile = "" + +} diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config new file mode 100644 index 0000000..24bd660 --- /dev/null +++ b/tests/config/nextflow.config @@ -0,0 +1,62 @@ +params { + outdir = "output/" + publish_dir_mode = "copy" + singularity_pull_docker_container = false + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' +} + +process { + resourceLimits = [ + cpus: 4, + memory: '16.GB', + time: '1.h' + ] +} + +profiles { + singularity { + singularity.enabled = true + singularity.autoMounts = true + singularity.registry = 'quay.io' + } + + conda { + conda.enabled = true + conda.channels = ['conda-forge', 'bioconda'] + conda.createTimeout = "120 min" + } + + mamba { + conda.enabled = true + conda.useMamba = true + conda.channels = ['conda-forge', 'bioconda'] + conda.createTimeout = "120 min" + } + + micromamba { + conda.enabled = true + conda.useMicromamba = true + conda.channels = ['conda-forge', 'bioconda'] + conda.createTimeout = "120 min" + } + + podman { + podman.enabled = true + podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" + podman.registry = 'quay.io' + } + + docker { + docker.enabled = true + docker.fixOwnership = true + docker.runOptions = '--platform=linux/amd64' + docker.registry = 'quay.io' + } +} + +// Load test_data.config containing paths to test data +includeConfig 'test_data.config' + +manifest { + nextflowVersion = '!>=24.10.2' +} diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config new file mode 100644 index 0000000..3a1cca8 --- /dev/null +++ b/tests/config/nf-test.config @@ -0,0 +1,98 @@ +params { + publish_dir_mode = "copy" + singularity_pull_docker_container = false + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +} + +process { + cpus = 2 + memory = '4.GB' + time = '2.h' +} + +profiles { + conda { + conda.enabled = true + conda.channels = ['conda-forge', 'bioconda'] + apptainer.enabled = false + } + mamba { + conda.enabled = true + conda.useMamba = true + } + micromamba { + conda.enabled = true + conda.useMicromamba = true + } + docker { + docker.enabled = true + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } + docker_self_hosted { + docker.enabled = true + docker.fixOwnership = true + docker.runOptions = '--platform=linux/amd64' + } + arm64 { + process.arch = 'arm64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/arm64' + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + } + podman { + podman.enabled = true + podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" + } + shifter { + shifter.enabled = true + } + charliecloud { + charliecloud.enabled = true + } + apptainer { + apptainer.enabled = true + apptainer.autoMounts = true + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + gitpod { + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB + } + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' + } +} + +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Increase time available to build Conda environment +conda { createTimeout = "120 min" } + +// Load test_data.config containing paths to test data +includeConfig 'test_data.config' + +manifest { + nextflowVersion = '!>=24.10.2' +} diff --git a/tests/config/test_data.config b/tests/config/test_data.config new file mode 100644 index 0000000..104b8ec --- /dev/null +++ b/tests/config/test_data.config @@ -0,0 +1,904 @@ +// README: +// https://github.com/nf-core/test-datasets/blob/modules/README.md + +params { + // Base directory for test data + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" + + test_data { + 'sarscov2' { + 'genome' { + genome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta" + genome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz" + genome_fasta_fai = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai" + genome_fasta_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst" + genome_dict = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3" + genome_gff3_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz" + genome_gtf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gtf" + genome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.paf" + genome_sizes = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.sizes" + transcriptome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta" + transcriptome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf" + proteome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta" + proteome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz" + + test_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed" + test_bedpe = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bedpe" + test_bed_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz" + test2_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed" + test_bed12 = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12" + baits_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed" + bed_autosql = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as" + + reference_cnn = "${params.test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn" + + kraken2 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2" + kraken2_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + + kraken2_bracken = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken" + kraken2_bracken_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" + + kaiju = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju" + kaiju_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz" + + kofamscan_profiles_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" + kofamscan_ko_list_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" + + metamaps_db = "${params.test_data_base}/data/genomics/sarscov2/genome/db/metamaps_db.tar.gz" + + ncbi_taxmap_zip = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" + taxon_list_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" + + mmseqs_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz" + + resfinder_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz" + + all_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas" + informative_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas" + + contigs_genome_maf_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" + contigs_genome_par = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par" + lastdb_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" + + baits_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list" + targets_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list" + regions_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt" + lc_extrap_mr = "${params.test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr" + } + 'illumina' { + test_single_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_single_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" + test_single_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" + test_paired_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_methylated_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" + test_paired_end_methylated_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" + test_paired_end_methylated_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" + test_unaligned_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" + test_interleaved_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" + test_1_fastq_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" + test_methylated_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" + test_methylated_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" + test_1_fastq_gz_fastqc_html = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html" + test_1_fastq_gz_fastqc_zip = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + + test_bedgraph = "${params.test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph" + + test_bigwig = "${params.test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig" + + test_wig_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" + + test_computematrix_mat_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" + + test_bcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf" + + test_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf" + test_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz" + test_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" + test2_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf" + test2_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + test2_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + test2_vcf_targets_tsv_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" + test3_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf" + test3_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz" + test3_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" + + contigs_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta" + scaffolds_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" + + assembly_gfa = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa" + assembly_gfa_bgz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" + assembly_gfa_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" + assembly_gfa_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" + + test_single_end_bam_readlist_txt = "${params.test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" + + SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" + } + 'nanopore' { + test_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam" + test_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" + + fast5_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" + + test_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz" + + test2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test_2.fastq.gz" + + test_sequencing_summary = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" + + test2_sequencing_summary = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test2.sequencing_summary.txt" + } + 'metagenome' { + classified_reads_assignment = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" + kraken_report = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" + krona_taxonomy = "${params.test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab" + seqid2taxid_map = "${params.test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map" + nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp" + names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/names.dmp" + prot_nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp" + prot_names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp" + prot_accession2taxid_gz = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz" + } + } + 'mus_musculus' { + 'genome' { + rnaseq_samplesheet = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" + rnaseq_genemeta = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" + rnaseq_contrasts = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" + rnaseq_matrix = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" + rnaseq_lengths = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv" + deseq_results = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" + genome_19_fasta = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz" + genome_19_gtf = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz" + } + 'illumina' { + test_1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" + genome_config = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json" + multiome_lib_csv = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv" + test_scARC_gex_R1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_gex_R2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_R1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_atac_R2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_I2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz" + } + 'csv' { + count_table = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv" + library = "${params.test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv" + } + 'txt' { + design_matrix = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt" + } + } + 'homo_sapiens' { + 'genome' { + 'riboseq' { + genome_gtf_20 = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf" + genome_fasta_20 = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz" + genome_alignment_bam = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bam" + genome_alignment_bai = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888_chr20.bai" + transcriptome_alignment_bam = "${params.test_data_base}/data/genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780888.Aligned.toTranscriptome.out.bam" + } + } + '10xgenomics' { + cellranger { + test_10x_10k_pbmc_5fb_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5fb_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv" + + test_10x_10k_pbmc_cmo_cmo_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_cmo_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv" + + test_10x_5k_cmvpos_tcells_ab_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_ab_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" + + test_10x_vdj_ref_json = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json" + test_10x_vdj_ref_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa" + test_10x_vdj_ref_suppfasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa" + + test_scATAC_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz" + test_scATAC_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz" + test_scATAC_3_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz" + test_scATAC_I_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz" + + test_10x_matrix_rna_raw_h5 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/438-21-raw_feature_bc_matrix.h5" + test_10x_matrix_hto_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/438_21_raw_HTO.csv" + + test_10x_sc3_v3_5k_a549_gex_l1_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L001_R1_001.fastq.gz" + test_10x_sc3_v3_5k_a549_gex_l1_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L001_R2_001.fastq.gz" + test_10x_sc3_v3_5k_a549_gex_l2_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L002_R1_001.fastq.gz" + test_10x_sc3_v3_5k_a549_gex_l2_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/gex/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_gex_S5_L002_R2_001.fastq.gz" + test_10x_sc3_v3_5k_a549_crispr_l1_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L001_R1_001.fastq.gz" + test_10x_sc3_v3_5k_a549_crispr_l1_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L001_R2_001.fastq.gz" + test_10x_sc3_v3_5k_a549_crispr_l2_fastq1 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L002_R1_001.fastq.gz" + test_10x_sc3_v3_5k_a549_crispr_l2_fastq2 = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/sc3_v3_5k_a549_gex_crispr/fastqs/crispr/subsampled_SC3_v3_NextGem_DI_CRISPR_A549_5K_crispr_S4_L002_R2_001.fastq.gz" + + } + spaceranger { + test_10x_ffpe_cytassist_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_cytassist_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_cytassist_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif" + test_10x_ffpe_cytassist_probeset = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv" + + test_10x_ffpe_v1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_v1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_v1_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" + } + } + 'genome' { + genome_elfasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta" + genome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta" + genome_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" + genome_fasta_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz" + genome_fasta_gz_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai" + genome_fasta_gz_gzi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi" + genome_strtablefile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip" + genome_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3" + genome_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf" + genome_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list" + genome_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed" + genome_blacklist_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed" + genome_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes" + genome_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed" + genome_header = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.header" + genome_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz" + genome_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi" + genome_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites" + transcriptome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta" + genome2_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta" + genome_chain_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz" + genome_annotated_interval_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv" + genome_mt_gb = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb" + genome_preprocessed_count_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv" + genome_preprocessed_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list" + genome_ploidy_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz" + genome_ploidy_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz" + genome_germline_cnv_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz" + genome_germline_cnv_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz" + genome_motifs = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt" + genome_config = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json" + + genome_1_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz" + genome_1_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf" + + genome_21_sdf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" + genome_21_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + genome_21_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + genome_21_gencode_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf" + genome_21_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" + genome_21_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_annotated_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed" + genome_21_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_antitarget_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" + genome_21_multi_interval_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" + genome_21_chromosomes_dir = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + genome_21_reference_cnn = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" + genome_21_eigenstrat_snp = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp" + genome_21_stitch_posfile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv" + + dbsnp_146_hg38_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" + dbsnp_146_hg38_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_146_hg38_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + gnomad_r2_1_1_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + mills_and_1000g_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + syntheticvcf_short_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" + syntheticvcf_short_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + syntheticvcf_short_score = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" + gnomad_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" + gnomad2_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" + genmod_compound_vcf_mt = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/genmod_compound.vcf" + + hapmap_3_3_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" + res_1000g_omni2_5_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" + res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" + res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" + res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" + dbsnp_138_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_138_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + gnomad_r2_1_1_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + mills_and_1000g_indels_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + haplotype_map = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" + dbNSFP_4_1a_21_hg38_txt_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz" + dbNSFP_4_1a_21_hg38_txt_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi" + ngscheckmate_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" + + index_salmon = "${params.test_data_base}/data/genomics/homo_sapiens/genome/index/salmon" + repeat_expansions = "${params.test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json" + justhusky_ped = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" + justhusky_minimal_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" + justhusky_minimal_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" + + vcfanno_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" + vcfanno_toml = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" + updsites_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed" + + prg_input = "${params.test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip" + crispr_functional_counts = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv" + crispr_functional_library = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv" + + vep_cache = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz" + affy_array_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv" + affy_array_celfiles_tar = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar" + + } + 'pangenome' { + pangenome_fa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa" + pangenome_fa_bgzip = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz" + pangenome_fa_bgzip_fai = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai" + pangenome_fa_bgzip_gzi = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" + pangenome_paf = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf" + pangenome_paf_gz = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz" + pangenome_panacus_tsv = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv" + pangenome_seqwish_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa" + pangenome_smoothxg_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" + pangenome_gfaffix_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" + 'odgi' { + pangenome_og = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og" + pangenome_lay = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay" + } + } + 'illumina' { + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" + test_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" + test_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" + test_paired_end_markduplicates_sorted_referencesn_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" + test_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" + test_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" + test_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" + test_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" + test_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" + test_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" + test_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" + test_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + test_paired_end_hla = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" + test_paired_end_hla_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" + test_paired_end_hla_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" + test_rna_paired_end_sorted_chr6_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam" + test_rna_paired_end_sorted_chr6_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai" + + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" + test2_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" + test2_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" + test2_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" + test2_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" + test2_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" + test2_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" + test2_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" + test2_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" + test2_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" + test2_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" + test2_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + test_paired_end_duplex_umi_unmapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" + test_paired_end_duplex_umi_mapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" + test_paired_end_duplex_umi_mapped_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" + test_paired_end_duplex_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" + test_paired_end_duplex_umi_duplex_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" + + mitochon_standin_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" + mitochon_standin_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" + test_illumina_mt_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam" + test_illumina_mt_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai" + + test3_single_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" + + read_group_settings_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" + + test_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" + test_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" + test_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" + test_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" + test_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" + test_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" + + test2_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" + test2_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" + test2_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" + test2_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" + test2_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" + test2_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" + test3_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram" + test3_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" + test_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" + test_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" + test_airrseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz" + test_airrseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" + test2_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" + test2_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" + test_rnaseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" + test_rnaseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" + test_paired_end_duplex_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" + test_paired_end_duplex_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" + test2_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + test_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table" + test2_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" + + test_paired_end_sorted_dragstrmodel = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" + + test_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" + test_pon_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" + + test2_haplotc_ann_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" + test2_haplotc_ann_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test_haplotc_cnn_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" + test_haplotc_cnn_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" + + test2_haplotc_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" + test2_haplotc_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" + + test2_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" + test2_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" + test2_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" + test2_allele_specific_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" + test2_allele_specific_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" + test2_allele_specific_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" + + test_test2_paired_mutect2_calls_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" + test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" + test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" + test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" + test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" + test_test2_paired_segmentation_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" + test_test2_paired_contamination_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" + + test_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" + test_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" + test_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" + test_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" + + test_genome_vcf_ud = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" + test_genome_vcf_mu = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" + test_genome_vcf_bed = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" + + test2_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" + test2_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" + test2_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" + test2_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + + test_genome21_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + + test_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" + test2_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" + + test_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" + test2_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" + + test_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" + test2_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" + + test_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak" + test2_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak" + + cutandrun_bedgraph_test_1 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" + cutandrun_bedgraph_test_2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" + na24385_chr22_coverage = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed" + + empty_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz" + empty_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi" + + simulated_sv = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz" + simulated_sv_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi" + simulated_sv2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz" + simulated_sv2_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi" + + test_rnaseq_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" + test_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" + test_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi" + na24385_chr22_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz" + na24385_chr22_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi" + genmod_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" + genmod_annotate_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" + genmod_models_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" + genmod_score_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" + + test_mito_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" + + test_pytor = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor" + rank_model = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" + + test_flowcell = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" + test_flowcell_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" + + varlociraptor_scenario = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml" + + test_interop_bcl2fastqstats_flowcell = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/interop_bcl2fastqstats/test_flowcell_stats.tar.gz" + + contig_ploidy_priors_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" + + purecn_ex1_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam" + purecn_ex1_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai" + purecn_ex1_interval = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt" + purecn_ex1_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz" + purecn_ex2_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz" + purecn_normalpanel_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz" + purecn_normalpanel_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi" + } + 'lexogen' { + i1_read_1 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_read_1.fastq.gz" + i1_read_2 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_read_2.fastq.gz" + i1_sample_sheet = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i1_sample_sheet.csv" + i5_i1_read_1 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_read_1.fastq.gz" + i5_i1_read_2 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_read_2.fastq.gz" + i5_i1_sample_sheet = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i5_i1_sample_sheet.csv" + i7_i1_read_1 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_read_1.fastq.gz" + i7_i1_read_2 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_read_2.fastq.gz" + i7_i1_sample_sheet = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i1_sample_sheet.csv" + i7_i5_i1_read_1 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_read_1.fastq.gz" + i7_i5_i1_read_2 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_read_2.fastq.gz" + i7_i5_i1_sample_sheet = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_i1_sample_sheet.csv" + i7_i5_read_1 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_read_1.fastq.gz" + i7_i5_read_2 = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_read_2.fastq.gz" + i7_i5_sample_sheet = "${params.test_data_base}/data/genomics/homo_sapiens/lexogen/idemux/i7_i5_sample_sheet.csv" + } + 'pacbio' { + primers = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta" + alz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam" + alzpbi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" + ccs = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" + ccs_fa = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" + ccs_fa_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" + ccs_fq = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" + ccs_fq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" + ccs_xml = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" + hifi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" + lima = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" + refine = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" + cluster = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" + singletons = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" + aligned = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" + alignedbai = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" + genemodel1 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" + genemodel2 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" + filelist = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt" + tag = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam" + } + 'popgen' { + plink_case_control_bed = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bed" + plink_case_control_bim = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bim" + plink_case_control_fam = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.fam" + plink_case_control_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.vcf.gz" + plink_case_control_bcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.bcf.gz" + plink_simulated_phe = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.phe" + plink_simulated_phenoname = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe" + plink_random_selected_snp = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_random_selected_snp.txt" + plink_simulated_pgen = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.pgen" + plink_simulated_psam = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.psam" + plink_simulated_pvar = "${params.test_data_base}/data/genomics/homo_sapiens/popgen/plink_simulated.pvar" + } + 'scramble' { + fasta = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa" + fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai" + bam = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam" + bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai" + cram = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram" + cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai" + bed = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bed" + } + 'gene_set_analysis' { + gct = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct" + cls = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls" + gmx = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx" + } + 'cnvkit' { + amplicon_cnr = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr" + amplicon_cns = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns" + } + 'demultiplexing' { + bam = "${params.test_data_base}/data/genomics/homo_sapiens/demultiplexing/chr21.bam" + donor_genotype = "${params.test_data_base}/data/genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf" + } + } + 'actinidia_chinensis' { + 'genome' { + genome_1_fasta_gz = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" + genome_1_gff3_gz = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gff3.gz" + genome_1_gtf_gz = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.gtf.gz" + genome_1_hints_gff_gz = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.hints.gff.gz" + } + } + 'bacteroides_fragilis' { + 'genome' { + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_gbff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" + genome_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" + genome_gff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" + + } + 'hamronization' { + genome_abricate_tsv = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" + genome_mapping_potential_arg = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" + } + 'illumina' { + test1_contigs_fa_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" + test1_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" + test1_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" + test1_contigs_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam" + test1_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" + test1_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" + test1_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" + test2_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" + test1_contigs_coverage_stats = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/coverage/test1_contigs.coverage.stats.txt" + test1_contigs_ids_tsv = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/tsv/test1_contigs_ids.tsv" + } + 'nanopore' { + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" + overlap_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" + } + } + 'candidatus_portiera_aleyrodidarum' { + 'genome' { + genome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" + genome_sizes = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" + proteome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" + test1_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" + test2_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" + test3_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" + } + 'illumina' { + test_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" + test_se_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" + } + 'nanopore' { + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" + } + } + 'haemophilus_influenzae' { + 'genome' { + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" + } + } + 'metagenome' { + 'taxonomy' { + sink_taxid_csv = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sink_taxid.csv" + sources_taxid_csv = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sources_labels.csv" + sources_labels_csv = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/sources_taxid.csv" + taxa_sqlite = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite.xz" + taxa_sqlite_traverse_pkl = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite_traverse.pkl" + } + } + 'streptococcus_agalactiae' { + 'genome' { + emu_db = "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/genome/emu" + } + 'nanopore' { + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/nanopore/fastq/test.fastq.gz" + } + } + 'saccharomyces_cerevisiae' { + 'genome' { + samplesheet = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv" + genome_gfp_gtf = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf" + kallisto_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz" + salmon_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz" + } + } + 'generic' { + 'csv' { + test_csv = "${params.test_data_base}/data/generic/csv/test.csv" + } + 'notebooks' { + rmarkdown = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" + ipython_md = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md" + ipython_ipynb = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb" + quarto_r = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_r.qmd" + quarto_python = "${params.test_data_base}/data/generic/notebooks/quarto/quarto_python.qmd" + } + 'tar' { + tar_gz = "${params.test_data_base}/data/generic/tar/hello.tar.gz" + } + 'tsv' { + test_tsv = "${params.test_data_base}/data/generic/tsv/test.tsv" + expression = "${params.test_data_base}/data/generic/tsv/expression.tsv" + network = "${params.test_data_base}/data/generic/tsv/network.tsv" + } + 'txt' { + hello = "${params.test_data_base}/data/generic/txt/hello.txt" + } + 'cooler'{ + test_pairix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" + test_pairix_pair_gz_px2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" + test_pairs_pair = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" + test_tabix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" + test_tabix_pair_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" + hg19_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" + test_merge_cool = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" + test_merge_cool_cp2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" + + } + 'pairtools' { + mock_4dedup_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam" + mock_4flip_pairs = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs" + mock_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes" + mock_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam" + mock_sam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam" + frag_bed = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed" + } + 'estsfs'{ + config_file = "${params.test_data_base}/data/delete_me/estsfs/config-JC.txt" + data_file = "${params.test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT" + seed_file = "${params.test_data_base}/data/delete_me/estsfs/seedfile.txt" + } + 'config' { + agat_config = "${params.test_data_base}/data/generic/config/agat_config.yaml" + config_network_datavzrd = "${params.test_data_base}/data/generic/config/config_network.datavzrd.yaml" + config_test_datavzrd = "${params.test_data_base}/data/generic/config/config_test.datavzrd.yaml" + ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + wittyer_config = "${params.test_data_base}/data/generic/config/wittyer_config.json" + } + 'unsorted_data' { + 'unsorted_text' { + genome_file = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome" + intervals = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed" + numbers_csv = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv" + } + } + } + 'proteomics' { + 'msspectra' { + ups_file1 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw" + ups_file2 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw" + profile_spectra = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML" + hla2_file = "${params.test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw" + } + 'database' { + yeast_ups = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta" + swissprot = "${params.test_data_base}/data/proteomics/database/UP000005640_9606.fasta" + } + 'maxquant' { + mq_contrasts = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" + mq_proteingroups = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt" + mq_samplesheet = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv" + mq_proteus_mat = "${params.test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv" + } + 'parameter' { + maxquant = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml" + sage_base_config = "${params.test_data_base}/data/proteomics/parameter/sage_base_config.json" + } + 'openms' { + idxml1 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML" + idxml2 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML" + } + 'pdb' { + tim1_pdb = "${params.test_data_base}/data/proteomics/pdb/1tim.pdb" + tim8_pdb = "${params.test_data_base}/data/proteomics/pdb/8tim.pdb" + } + } + 'galaxea_fascicularis' { + hic { + pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext" + } + } + 'deilephila_porcellus' { + 'mito' { + ref_fa = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta" + ref_gb = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb" + hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa" + contigs = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa" + } + } + 'arabidopsis_thaliana' { + 'plastid' { + hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta" + } + } + + 'imaging' { + 'h5' { + plant_wga = "${params.test_data_base}/data/imaging/h5/plant_wga.h5" + plant_wga_prob = "${params.test_data_base}/data/imaging/h5/plant_wga_probabilities.h5" + } + 'ilp' { + plant_wga_multicut = "${params.test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp" + plant_wga_pixel_class = "${params.test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp" + } + 'tiff' { + mouse_heart_wga = "${params.test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff" + } + 'ome-tiff' { + cycif_tonsil_channels = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv" + cycif_tonsil_cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycif_tonsil_cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + cycif_tonsil_cycle3 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif" + cycif_tonsil_dfp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif" + cycif_tonsil_ffp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif" + } + 'registration' { + markers = "${params.test_data_base}/data/imaging/registration/markers.csv" + cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + } + 'segmentation' { + markers = "${params.test_data_base}/data/imaging/segmentation/markers.csv" + image = "${params.test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif" + nuclear_image = "${params.test_data_base}/data/imaging/segmentation/nuclear_image.tif" + } + 'quantification' { + markers = "${params.test_data_base}/data/imaging/quantification/markers.csv" + image = "${params.test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif" + mask = "${params.test_data_base}/data/imaging/quantification/cell.ome.tif" + } + 'downstream' { + markers = "${params.test_data_base}/data/imaging/downstream/markers.csv" + cell_feature_array = "${params.test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv" + phenotyped = "${params.test_data_base}/data/imaging/downstream/phenotyped.csv" + 'celesta' { + data = "${params.test_data_base}/data/imaging/downstream/celesta/img_data.csv" + signature = "${params.test_data_base}/data/imaging/downstream/celesta/signature_matrix.csv" + thresholds = "${params.test_data_base}/data/imaging/downstream/celesta/thresholds_celesta.csv" + } + } + 'background_subtraction' { + markers = "${params.test_data_base}/data/imaging/background_subtraction/markers.csv" + image = "${params.test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif" + } + 'core_detection' { + image = "${params.test_data_base}/data/imaging/core_detection/single_core_dapi.tif" + } + 'spot_detection' { + image = "${params.test_data_base}/data/imaging/spot_detection/immunofluorescence.tif" + } + 'staging' { + folder = "${params.test_data_base}/data/imaging/staging/phenoimager/" + file1 = "${params.test_data_base}/data/imaging/staging/phenoimager/tile1.tif" + file2 = "${params.test_data_base}/data/imaging/staging/phenoimager/tile2.tif" + } + 'imc_staging' { + text = "${params.test_data_base}/data/imaging/staging/imaging_mass_cytometry/acquisition.txt" + } + } + } +}