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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"
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: MALTEXTRACT (#725) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start maltextract module * start tests * Get tests working now we have test data * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Changes after review * Update tests/modules/maltextract/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/maltextract/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/maltextract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-21 18:57:27 +00:00
ncbi_taxmap_zip = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
taxon_list_txt = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
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"
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
SRR13255544_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
SRR11140744_tar_gz = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR11140744.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
}
'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"
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 08:02:30 +00:00
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
Add compressed bed files (#864) * add cram files to config * Update tests/config/test_data.config * Add compressed bed file Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-15 09:10:53 +00:00
genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
updated paths to test data (#478) * updated paths to test data * Update test_data.config changed file names
2021-05-03 06:13:07 +00:00
transcriptome_fasta = "${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 = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
}
Fix some module tests after switching to config data (#386) * Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
'illumina' {
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 08:02:30 +00:00
test_paired_end_sorted_bam = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
test_paired_end_markduplicates_sorted_referencesn_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
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"
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_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"
Add cram files to config (#862) * add cram files to config * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-15 08:40:16 +00:00
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
test2_paired_end_markduplicates_sorted_cram_crai = "${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"
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${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"
new module: gatk4/calculatecontamination (#778) * initiated files for calculate contamination * pushing local repo to remote * created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data * added option and tests for outputting optional segmentation file * saving for test push * versions updated, test data added * Update main.nf * fixed versions info, should report correctly now * small update to main.nf outputs formatting * Apply suggestions from code review * Update test_data.config * Apply suggestions from code review Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:52:00 +00:00
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"
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
Learnreadorientationmodel (#794) * files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-07 12:55:06 +00:00
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
Learnreadorientationmodel (#794) * files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-07 12:55:06 +00:00
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 14:30:43 +00:00
test_genome_vcf = "${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"
New module: `LIMA` (#719) * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 🐛 FIX: Clean test_data.config * Update modules/lima/main.nf Add meta to each output Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/lima/main.nf Remove useless parenthesis Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 🐛 FIX: Keep version number only * 🐛 FIX: Reintegrate prefix variable and use it to define output file name * 👌 IMPROVE: add suffix arg to check output files names * 👌 IMPROVE: Use prefix for output filename * 🐛 FIX: Set optional output Allow usage of different input formats * 👌 IMPROVE: Update meta file * 👌 IMPROVE: Update test One test for each input file type * 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files * 👌 IMPROVE: Update with last templates / Follow new version.yaml rule * 🐛 FIX: Fix typos and include getProcessName function * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Using suffix to manage output was not a my best idea Add a bash code to detect extension and update output file name * 👌 IMPROVE: clean code Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-09-27 15:14:35 +00:00
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"
few version and test data config fixes (#758) * update kleborate version info * fix stderr capture * few more version fixes * fix version info on more tools
2021-09-28 19:42:04 +00:00
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
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
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
}
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