nf-core_modules/tests/data/README.md

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)
  • 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
  • table:
    • 'test.table': Recalibration table generated with gatk4 BaseRecalibrator from 'test_paired_end.sorted.bam', using 'test.vcf.gz' as known sites.
  • 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