mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
20d8250d9f
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
336 lines
35 KiB
Text
336 lines
35 KiB
Text
// Base directory for test data
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def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data"
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params {
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test_data {
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'sarscov2' {
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'genome' {
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genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
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genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
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genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
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genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
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genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
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genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
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genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
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genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
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transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
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transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
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test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
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test_bed_gz = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed.gz"
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test2_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed"
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test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
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baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
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kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
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kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
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ncbi_taxmap_zip = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
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taxon_list_txt = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
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all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
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informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
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contigs_genome_maf_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz"
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contigs_genome_par = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.par"
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lastdb_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"
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baits_interval_list = "${test_data_dir}/genomics/sarscov2/genome/picard/baits.interval_list"
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targets_interval_list = "${test_data_dir}/genomics/sarscov2/genome/picard/targets.interval_list"
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}
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'illumina' {
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test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.bam"
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test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam"
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test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai"
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test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.bam"
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test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
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test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
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test_paired_end_methylated_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam"
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test_paired_end_methylated_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam"
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test_paired_end_methylated_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai"
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test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.unaligned.bam"
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test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
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test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
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test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
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test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
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test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz"
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test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
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test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
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test_bigwig = "${test_data_dir}/genomics/sarscov2/illumina/bigwig/test.bigwig"
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test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz"
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test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
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test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
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test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
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test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
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test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
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test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf"
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test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
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test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
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test2_vcf_targets_tsv_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz"
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test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
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test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
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test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
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contigs_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta"
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scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
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assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
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test_single_end_bam_readlist_txt = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
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SRR13255544_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
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SRR11140744_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
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}
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'nanopore' {
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test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"
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test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
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fast5_tar_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fast5/fast5.tar.gz"
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test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
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test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
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}
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}
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'homo_sapiens' {
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'genome' {
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genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta"
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genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai"
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genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict"
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genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
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genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
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genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
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genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
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genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
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genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
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genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
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genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
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transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
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genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
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genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
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dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
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dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
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gnomad_r2_1_1_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
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gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
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mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
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mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
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syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
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syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
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index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
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repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
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justhusky_ped = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
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justhusky_minimal_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
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justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
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}
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'illumina' {
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test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
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test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
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test_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam"
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test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
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test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
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test_paired_end_markduplicates_sorted_referencesn_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
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test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
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test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
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test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
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test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
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test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
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test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
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test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
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test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
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test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
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test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
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test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
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test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
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test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
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test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
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test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
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test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
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test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
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test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
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test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
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test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
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test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
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test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
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test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
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test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
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test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
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test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
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test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
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test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
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test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
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test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
|
|
test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
|
|
test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
|
|
|
|
test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
|
|
test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
|
|
test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
|
|
test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
|
|
test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
|
|
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
|
|
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
|
|
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
|
|
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz"
|
|
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
|
|
|
|
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
|
|
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
|
|
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
|
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
|
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
|
|
|
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
|
|
|
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
|
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
|
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
|
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
|
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
|
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
|
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
|
|
|
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
|
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
|
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
|
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
|
|
|
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
|
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
|
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
|
|
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
|
|
|
|
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
|
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
|
|
|
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
|
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
|
|
|
|
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
|
|
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
|
|
|
|
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
|
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
|
|
|
|
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
|
|
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
|
|
}
|
|
'pacbio' {
|
|
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
|
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
|
|
alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
|
|
ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
|
|
ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
|
|
ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
|
|
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
|
|
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
|
|
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
|
|
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
|
|
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
|
|
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
|
|
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
|
|
singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
|
|
aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
|
|
alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
|
|
genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
|
|
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
|
|
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
|
|
}
|
|
}
|
|
'bacteroides_fragilis' {
|
|
'genome' {
|
|
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
|
|
genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
|
|
}
|
|
'illumina' {
|
|
test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
|
|
test1_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
|
|
test1_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
|
|
test2_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
|
|
test2_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
|
|
test1_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam"
|
|
test1_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
|
|
test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
|
|
test2_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam"
|
|
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
|
|
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
|
|
}
|
|
'nanopore' {
|
|
test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
|
|
overlap_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf"
|
|
}
|
|
}
|
|
'candidatus_portiera_aleyrodidarum' {
|
|
'genome' {
|
|
genome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta"
|
|
genome_sizes = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes"
|
|
genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz"
|
|
genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk"
|
|
proteome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta"
|
|
test1_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff"
|
|
test2_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff"
|
|
test3_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
|
|
}
|
|
'illumina' {
|
|
test_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fasta/test_1.fastq.gz"
|
|
test_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
|
|
test_se_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
|
|
}
|
|
'nanopore' {
|
|
test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz"
|
|
}
|
|
}
|
|
'haemophilus_influenzae' {
|
|
'genome' {
|
|
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz"
|
|
genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz"
|
|
genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
|
|
}
|
|
}
|
|
'generic' {
|
|
'csv' {
|
|
test_csv = "${test_data_dir}/generic/csv/test.csv"
|
|
}
|
|
'notebooks' {
|
|
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
|
|
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
|
|
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
|
|
}
|
|
'tsv' {
|
|
test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
|
|
}
|
|
'txt' {
|
|
hello = "${test_data_dir}/generic/txt/hello.txt"
|
|
}
|
|
'cnn' {
|
|
reference = "${test_data_dir}/generic/cnn/reference.cnn"
|
|
}
|
|
'cooler'{
|
|
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
|
|
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
|
|
test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
|
|
test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
|
|
test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
|
|
hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
|
|
test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
|
|
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
|
|
|
|
}
|
|
}
|
|
}
|
|
}
|