nf-core_modules/tests/data/README.md
Kevin Menden a90332906b
add mergebamalignment (#259)
* 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>
2021-03-17 15:56:56 +01:00

54 lines
3.2 KiB
Markdown
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

# Modules Test Data
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`.
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.
## Data Description
### genomics
* sarscov2
* bam:
* 'test_{,methylated}_paired_end.bam': sarscov2 sequencing reads aligned against test_genomic.fasta using minimap2
* 'test_{,methylated}_paired_end.sorted.bam': sorted version of the above bam file
* 'test_{,methylated}_paired_end.bam.sorted.bam.bai': bam index for the sorted bam file
* 'test_single_end.bam': alignment (unsorted) of the 'test_1.fastq.gz' reads against test_genomic.fasta using minimap2
* 'test_unaligned.bam': unmapped BAM file created from 'test_1.fastq.gz' using GATK4 SamToFastq
* bed
* 'test.bed': exemplary bed file for the MT192765.1 genome (fasta/test_genomic.fasta)
* 'test.2.bed': slightly modified copy of the above file
* 'test.bed.gz': gzipped version
* 'test.genome.sizes': genome size for the MT192765.1 genome
* fasta
* 'test_genomic.fasta': MT192765.1 genomem including (GCA_011545545.1_ASM1154554v1)
* 'test_genomic.dict': GATK dict for 'test_genomic.fasta'
* 'test_genomic.fasta.fai': fasta index for 'test_genomic.fasta'
* 'test_cds_from_genomic.fasta': coding sequencing from MT192765.1 genome (transcripts)
* fastq
* 'test_{1,2}.fastq.gz' sarscov2 paired-end sequencing reads
* 'test_{1,2}.2.fastq.gz: copies of the above reads
* 'test_methylated_{1,2}.fastq.gz' sarscov2 paired-end bisulfite sequencing reads (generated with [Sherman](https://github.com/FelixKrueger/Sherman))
* gtf
* 'test_genomic.gtf': GTF for MT192765.1 genome
* 'test_genomic.gff3': GFF for MT192765.1 genome
* 'test_genomic.gff3.gz': bgzipped-version
* paf
* 'test_cds_from_genomic.paf': PAF file for MT192765.1 genome
* vcf
* 'test.vcf', 'test2.vcf': generated from 'test_paired_end.sorted.bam' using bcftools mpileup, call and filter
* 'test3.vcf': generated from 'test_single_end.sorted.bam' using bcftools mpileup, call and filter
* '*.gz': generated from VCF files using bgzip
* '.tbi': generated from '.vcf.gz' files using `tabix -p vcf -f <file>`
### generic
* 'a.gff3.gz': bgzipped gff3 file currently necessary for TABIX test
* bedgraph: bedgraph files for seacr
* fasta: additional fasta file currently necessary for STAR
* fastq: additional fastq files currently necessary for STAR
* gtf: additional gtf file for STAR
* vcf: several VCF files for tools using those, will be removed in the future
* 'test.txt.gar.gz' exemplary tar file for the untar module