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* add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
54 lines
3.2 KiB
Markdown
54 lines
3.2 KiB
Markdown
# Modules Test Data
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This directory contains all data used for the individual module tests. It is currently organised in `genomics` and `generic`. The former contains all typical data required for genomics modules, such as fasta, fastq and bam files. Every folder in `genomics` corresponds to a single organisms. Any other data is stored in `generic`. This contains files that currently cannot be associated to a genomics category, but also depreciated files which will be removed in the future and exchanged by files in `genomics`.
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When adding a new module, please check carefully whether the data necessary for the tests exists already in `tests/data/genomics`. If you can't find the data, please ask about it in the slack #modules channel.
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## Data Description
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### genomics
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* sarscov2
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* bam:
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* 'test_{,methylated}_paired_end.bam': sarscov2 sequencing reads aligned against test_genomic.fasta using minimap2
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* 'test_{,methylated}_paired_end.sorted.bam': sorted version of the above bam file
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* 'test_{,methylated}_paired_end.bam.sorted.bam.bai': bam index for the sorted bam file
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* 'test_single_end.bam': alignment (unsorted) of the 'test_1.fastq.gz' reads against test_genomic.fasta using minimap2
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* 'test_unaligned.bam': unmapped BAM file created from 'test_1.fastq.gz' using GATK4 SamToFastq
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* bed
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* 'test.bed': exemplary bed file for the MT192765.1 genome (fasta/test_genomic.fasta)
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* 'test.2.bed': slightly modified copy of the above file
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* 'test.bed.gz': gzipped version
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* 'test.genome.sizes': genome size for the MT192765.1 genome
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* fasta
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* 'test_genomic.fasta': MT192765.1 genomem including (GCA_011545545.1_ASM1154554v1)
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* 'test_genomic.dict': GATK dict for 'test_genomic.fasta'
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* 'test_genomic.fasta.fai': fasta index for 'test_genomic.fasta'
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* 'test_cds_from_genomic.fasta': coding sequencing from MT192765.1 genome (transcripts)
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* fastq
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* 'test_{1,2}.fastq.gz' sarscov2 paired-end sequencing reads
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* 'test_{1,2}.2.fastq.gz‘: copies of the above reads
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* 'test_methylated_{1,2}.fastq.gz' sarscov2 paired-end bisulfite sequencing reads (generated with [Sherman](https://github.com/FelixKrueger/Sherman))
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* gtf
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* 'test_genomic.gtf': GTF for MT192765.1 genome
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* 'test_genomic.gff3': GFF for MT192765.1 genome
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* 'test_genomic.gff3.gz': bgzipped-version
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* paf
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* 'test_cds_from_genomic.paf': PAF file for MT192765.1 genome
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* vcf
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* 'test.vcf', 'test2.vcf': generated from 'test_paired_end.sorted.bam' using bcftools mpileup, call and filter
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* 'test3.vcf': generated from 'test_single_end.sorted.bam' using bcftools mpileup, call and filter
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* '*.gz': generated from VCF files using bgzip
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* '.tbi': generated from '.vcf.gz' files using `tabix -p vcf -f <file>`
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### generic
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* 'a.gff3.gz': bgzipped gff3 file currently necessary for TABIX test
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* bedgraph: bedgraph files for seacr
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* fasta: additional fasta file currently necessary for STAR
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* fastq: additional fastq files currently necessary for STAR
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* gtf: additional gtf file for STAR
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* vcf: several VCF files for tools using those, will be removed in the future
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* 'test.txt.gar.gz' exemplary tar file for the untar module
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