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nf-core_modules/tests/config/test_data.config

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Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
// Base directory for test data
Iqtree (#435) * Resolve suggests after PR review * add newline to functions * need variable interpolation using double quotes; remove unnecessary tag * add a more resilient link to raw github files * remove trailing slash * Update software/iqtree/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 16:01:26 +00:00
def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
params {
test_data {
'sarscov2' {
'genome' {
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
module: unzip (#642) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add unzip module * Remove missing TODOs update mtea * Apply changes after code-review from @grst * Account for user trying to supply two input archives * Remove debugging test * Update modules/unzip/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Correct output path Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 07:40:57 +00:00
genome_fasta_zip = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.zip"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
test_bed_gz = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed.gz"
test2_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed"
test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
New last/train module to train alignment parameters. (#492) * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:37:08 +00:00
New module last/mafswap to reorder sequences in alignments (#500) * New module last/mafswap to reorder sequences in alignments The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reorders sequences in alignment files in Multiple Alignment Format. When run without command-line arguments, it will swap the target and the query sequences. This is useful when turning a many-to-many alignment into a many-to-one and then a one-to-one alignment in conjunction with the `last-split` command (split, swap, split and swap again). The LAST aligner outputs MAF files, but other tools also use this format. As MAF files can be very large (up to hundreds of gigabytes), the module expects its input to be compressed with gzip and will compress its output. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Update MD5 sum. Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of an empty file compressed with `gzip --no-name`… This happened because I forgot to update the config file after correcting the module… sorry ! * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change name as suggested in pull request. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:59:23 +00:00
contigs_genome_maf_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz"
New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:10:48 +00:00
contigs_genome_par = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.par"
New last/train module to train alignment parameters. (#492) * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:37:08 +00:00
lastdb_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
}
'illumina' {
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.bam"
test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam"
test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai"
test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.bam"
test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
test_paired_end_methylated_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam"
test_paired_end_methylated_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam"
test_paired_end_methylated_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai"
test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.unaligned.bam"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz"
test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_bigwig = "${test_data_dir}/genomics/sarscov2/illumina/bigwig/test.bigwig"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf"
test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
Add bcftools/view module (#669) * initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
2021-09-12 17:51:40 +00:00
test2_vcf_targets_tsv_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
contigs_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta"
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
module: picard filtersamreads (#602) * Start work filtersamreads * Refactored to allow optional input * Use proper readlist test data * Remove typo * Fix if else condition * Remove debugging code * Fix container URLs * Add required input specification meta * Cleanup * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fix suffixing * Additional formatting tweaks * Update modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/picard/filtersamreads/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 14:22:19 +00:00
test_single_end_bam_readlist_txt = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
}
'nanopore' {
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"
test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
module: picard filtersamreads (#602) * Start work filtersamreads * Refactored to allow optional input * Use proper readlist test data * Remove typo * Fix if else condition * Remove debugging code * Fix container URLs * Add required input specification meta * Cleanup * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fix suffixing * Additional formatting tweaks * Update modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/picard/filtersamreads/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 14:22:19 +00:00
fast5_tar_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fast5/fast5.tar.gz"
Add artic minion (#486) * Add artic minion module * Add fast5 to test data configuration * Add test for artic minion
2021-05-07 15:37:35 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
Nanoplot and sequencing_summary.txt for Nanopore test data (#364) * add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
2021-04-09 07:31:38 +00:00
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
}
}
'homo_sapiens' {
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
'genome' {
genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta"
genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai"
genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict"
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
updated paths to test data (#478) * updated paths to test data * Update test_data.config changed file names
2021-05-03 06:13:07 +00:00
transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
new module: pbccs (#688) * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 10:48:18 +00:00
genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
gnomad_r2_1_1_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
updated paths to test data (#478) * updated paths to test data * Update test_data.config changed file names
2021-05-03 06:13:07 +00:00
index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-08-16 15:47:42 +00:00
repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
}
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
'illumina' {
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
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"
Fix rsem (#555) * bump bcftools filter * fix bcftools * rsem/preparereference * added calculateexpression * meta.yml and pytest_software * paired end * add test.yml
2021-07-02 11:09:48 +00:00
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"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
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_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
test_genome_vcf_gz = "${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"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
Add gvcf index files (#472)
2021-04-28 19:23:10 +00:00
test2_genome_vcf_gz = "${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"
updated paths to test data (#478) * updated paths to test data * Update test_data.config changed file names
2021-05-03 06:13:07 +00:00
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_1.fastq.gz"
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_2.fastq.gz"
Add hifiasm module (#596) * Add hifiasm module * Tidy up module * Add pacbio files to test_data.config
2021-07-20 20:50:22 +00:00
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
}
'pacbio' {
new module: pbccs (#688) * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 10:48:18 +00:00
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"
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 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
}
}
}
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
}
Reference in a new issue Copy permalink