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nf-core / test-datasets

Test data to be used for automated testing with the nf-core pipelines
https://nf-co.re
MIT License
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Rearrange and rename the `delete_me` folder #1245

Open SPPearce opened 4 months ago

SPPearce commented 4 months ago

We currently have a folder called delete_me in the modules repo. This contains a wide range of files that have been deposited, mostly for specific modules. It is NOT included in the README file, so isn't clear what it actually contains and therefore doesn't get used. Some of it may no longer be used.

SPPearce commented 4 months ago

I would suggest that we go through the files in here, and provided they are being used in a module, we move them into a seperate category in the main body of the test-datasets.

SPPearce commented 4 months ago

There are currently about 50(!) modules with data in here:

adapterremoval/adapterremoval_adapterlist.txt
ampcombi/ampcombi2/sample_1_ampcombi.tsv
ampcombi/ampcombi2/sample_2_ampcombi.tsv
ampcombi/general_amps.fasta
ampcombi/general_amps.xlsx
ampcombi/test_faa.tar.gz
ampcombi/test_faa/sample_1.faa
ampcombi/test_faa/sample_2.faa
ampcombi/test_faa_0.2/sample_1.faa
ampcombi/test_faa_0.2/sample_2.faa
ampcombi/test_files.tar.gz
ampcombi/test_gbk_0.2/sample_1.gbff
ampcombi/test_gbk_0.2/sample_2.gbff
amrfinderplus/test_output.tsv
angsd/HapMapChrX.gz
antismash/css.tar.gz
antismash/detection.tar.gz
antismash/modules.tar.gz
baftest/test.baf.txt.gz
baftest/test.baf.txt.gz.tbi
bcftools/stats/exons.tsv.gz
beagle/plink.chr22.GRCh38.map
beagle/ref.22Jul22.46e.vcf.gz
beagle/target.22Jul22.46e.vcf.gz
bedgraph/IgG_1_to_chr20.bedgraph
bedgraph/K27me3_1_to_chr20.bedgraph
biscuit/test-cg.bed.gz
biscuit/test-snp.bed
biscuit/test-snp.bed.gz
biscuit/test.vcf.gz
bos_taurus/BSA_QC_file.idXML
bos_taurus/BSA_QC_file.raw
centrifuge/minigut_cf.1.cf
centrifuge/minigut_cf.2.cf
centrifuge/minigut_cf.3.cf
centrifuge/minigut_cf.4.cf
condensedepthevidence/testN.rd.txt.gz
condensedepthevidence/testN.rd.txt.gz.tbi
eggnogmapper/eggnog.db
epang/query.alnfaa.gz
epang/reference.alnfaa.gz
epang/reference.newick
estsfs/TEST-DATA.TXT
estsfs/config-JC.txt
estsfs/read_me.md
estsfs/seedfile.txt
fastp/adapters.fasta
fastq/test_R1.fastq.gz
fastq/test_R2.fastq.gz
fastq/test_single_end.fastq.gz
gappa/epa_result.jplace.gz
gappa/gappa_taxonomy.tsv
gappa/reference.root
gfa/B-3106.gfa
glimpse/1000GP.chr21.noNA12878.s.bcf
glimpse/1000GP.chr21.noNA12878.s.bcf.csi
glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz
glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi
glimpse/NA12878.chr21.s.1x.bam
glimpse/NA12878.chr21.s.1x.bam.bai
glimpse/NA12878.chr21.s.1x.cram
glimpse/NA12878.chr21.s.1x.cram.crai
glimpse/NA12878.chr21.s.1x.vcf.gz
glimpse/NA12878.chr21.s.1x.vcf.gz.csi
glimpse/NA12878.chr21.s.bcf
glimpse/NA12878.chr21.s.bcf.csi
glimpse/chr21.b38.gmap.gz
glimpse/hs38DH.chr21.fa.gz
glimpse/hs38DH.chr21.fa.gz.fai
glimpse/hs38DH.chr21.fa.gz.gzi
hapibd/excludeSamples.txt
hapibd/target.map
hapibd/target.truth.vcf.gz
hmmer/PF14720_seed.alnfaa.gz
hmmer/bac.16S_rRNA.hmm.gz
hmmer/e_coli_k12_16s.fna.gz
kaiju/names.dmp
kaiju/nodes.dmp
kaiju/proteins.fmi
kallistobustools/GRCm39.chr19_100k.fa.gz
kallistobustools/gencode.VM26.chr19_10k.gtf.gz
kmcp.tar.gz
kmcp/NC_045512.2.fasta
kmcp/kmcp_profile.tar.gz
kmcp/seqid2taxid.map
krona/kaiju_out4krona.txt
krona/ktimporttext.txt
malt/test.rma6
metabuli/README.md
metabuli/acc2taxid
metabuli/metabuli_db.tar.gz
metabuli/taxonomy/merged.dmp
metabuli/taxonomy/names.dmp
metabuli/taxonomy/nodes.dmp
metaphlan4_database.tar.gz
metaphlan_database.tar.gz
minigut_cf.tar.gz
nanomonsv/input_bam/test_ctrl.bam
nanomonsv/input_bam/test_ctrl.bam.bai
nanomonsv/input_bam/test_tumor.bam
nanomonsv/input_bam/test_tumor.bam.bai
partis/partisTestSmall.fa
pep/test_nextflow_original_samplesheet.csv
pep/test_pep_format_files/config.yaml
pep/test_pep_format_files/samplesheet.csv
pep/test_samplesheet_schema.yaml
preseq/SRR1003759_5M_subset.mr
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.hap.gz
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.legend.gz
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.samples
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.vcf.gz
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.vcf.gz.tbi
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.onlyNA12878.vcf.gz
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.onlyNA12878.vcf.gz.tbi
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.phasefile.txt
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.posfile.txt
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.vcf.gz
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.vcf.gz.tbi
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.vcf.gz.temp
quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.vcf.gz.temp.tbi
quilt/CEU-chr20-final.b38.txt.gz
quilt/NA12878.haplotagged.0.1.bam
quilt/NA12878.haplotagged.0.1.bam.bai
quilt/NA12878.haplotagged.1.0.bam
quilt/NA12878.haplotagged.1.0.bam.bai
quilt/NA12878.illumina.0.1.bam
quilt/NA12878.illumina.0.1.bam.bai
quilt/NA12878.illumina.1.0.bam
quilt/NA12878.illumina.1.0.bam.bai
quilt/NA12878.ont.0.1.bam
quilt/NA12878.ont.0.1.bam.bai
quilt/NA12878.ont.1.0.bam
quilt/NA12878.ont.1.0.bam.bai
quilt/bamlist.0.1.txt
quilt/bamlist.1.0.txt
rgi/.ncbirc
somalier/ancestry-labels-1kg.tsv
somalier/family.ped
somalier/groups.txt
somalier/normal.somalier
somalier/sites_chr21.hg38.vcf.gz
somalier/tumour.somalier
somalier/whole_genome.somalier
spades/spades_input_yml.yml
srst2/MLST_DB.fas
srst2/ResGANNCBI_20210507_srst2.fasta
srst2/SRR9067271_1.fastq.gz
srst2/SRR9067271_2.fastq.gz
srst2/Test_Sample_R1.fastq.gz
srst2/Test_Sample_R2.fastq.gz
srst2/profiles.csv
srst2/readme.md
srst2/resFinder_20180221_srst2.fasta
srst2/samplesheet.csv
svcluster/samples_ploidy.tsv
tailfindr/test.fast5
taxpasta/samplesheet.tsv
test.txt.tar.gz
tnfilter/sample4_vs_sample3.tnhaplotyper2.contamination_data.tsv
tnfilter/sample4_vs_sample3.tnhaplotyper2.orientation_data.tsv
tnfilter/sample4_vs_sample3.tnhaplotyper2.segments
tnfilter/sample4_vs_sample3.tnhaplotyper2.vcf.gz
tnfilter/sample4_vs_sample3.tnhaplotyper2.vcf.gz.stats
tnfilter/sample4_vs_sample3.tnhaplotyper2.vcf.gz.tbi
verifybamid/1000g.phase3.10k.b38.vcf.gz.dat.UD
verifybamid/1000g.phase3.10k.b38.vcf.gz.dat.V
verifybamid/1000g.phase3.10k.b38.vcf.gz.dat.bed
verifybamid/1000g.phase3.10k.b38.vcf.gz.dat.mu
verifybamid/test.genome.vcf.UD
verifybamid/test.genome.vcf.V
verifybamid/test.genome.vcf.bed
verifybamid/test.genome.vcf.mu
viennarna/rnacofold/test.fa