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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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If we are not allowing links to external git files, then we need to deal with all those files #1250

Open SPPearce opened 2 months ago

SPPearce commented 2 months ago

The current suggestion is that we shouldn't have links to external files hosted on git. If we don't want these, then we'll need to go through and do something with the tests for these files

SPPearce commented 2 months ago 
./modules/nf-core/adapterremoval/tests/main.nf.test
./modules/nf-core/ampcombi/tests/main.nf.test
./modules/nf-core/ampcombi2/cluster/tests/main.nf.test
./modules/nf-core/ampcombi2/complete/tests/main.nf.test
./modules/nf-core/ampcombi2/parsetables/tests/main.nf.test
./modules/nf-core/antismash/antismashlite/tests/main.nf.test
./modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test
./modules/nf-core/bases2fastq/tests/main.nf.test
./modules/nf-core/bcl2fastq/tests/main.nf.test
./modules/nf-core/bclconvert/tests/main.nf.test
./modules/nf-core/cat/fastq/tests/main.nf.test
./modules/nf-core/centrifuge/centrifuge/tests/main.nf.test
./modules/nf-core/centrifuge/kreport/tests/main.nf.test
./modules/nf-core/checkv/endtoend/tests/main.nf.test
./modules/nf-core/checkv/updatedatabase/tests/main.nf.test
./modules/nf-core/csvtk/concat/tests/main.nf.test
./modules/nf-core/csvtk/join/tests/main.nf.test
./modules/nf-core/dragmap/hashtable/tests/main.nf.test
./modules/nf-core/dragonflye/tests/main.nf.test
./modules/nf-core/eggnogmapper/tests/main.nf.test
./modules/nf-core/fastme/tests/main.nf.test
./modules/nf-core/fastqc/tests/main.nf.test
./modules/nf-core/flye/tests/main.nf.test
./modules/nf-core/gatk4/svcluster/tests/main.nf.test
./modules/nf-core/glimpse2/chunk/tests/main.nf.test
./modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test
./modules/nf-core/hmmer/hmmsearch/tests/main.nf.test
./modules/nf-core/igvreports/tests/main.nf.test
./modules/nf-core/iqtree/tests/main.nf.test
./modules/nf-core/magus/align/tests/main.nf.test
./modules/nf-core/magus/guidetree/tests/main.nf.test
./modules/nf-core/maltextract/tests/main.nf.test
./modules/nf-core/mindagap/duplicatefinder/tests/main.nf.test
./modules/nf-core/mlst/tests/main.nf.test
./modules/nf-core/mtmalign/align/tests/main.nf.test
./modules/nf-core/mudskipper/bulk/tests/main.nf.test
./modules/nf-core/multiqc/tests/main.nf.test
./modules/nf-core/muscle5/super5/tests/main.nf.test
./modules/nf-core/mygene/tests/main.nf.test
./modules/nf-core/narfmap/hashtable/tests/main.nf.test
./modules/nf-core/oatk/tests/main.nf.test
./modules/nf-core/pretextmap/tests/main.nf.test
./modules/nf-core/propr/grea/tests/main.nf.test
./modules/nf-core/propr/propd/tests/main.nf.test
./modules/nf-core/propr/propr/tests/main.nf.test
./modules/nf-core/quilt/quilt/tests/main.nf.test
./modules/nf-core/shovill/tests/main.nf.test
./modules/nf-core/spades/tests/main.nf.test
./modules/nf-core/tcoffee/align/tests/main.nf.test
./modules/nf-core/tcoffee/alncompare/tests/main.nf.test
./modules/nf-core/tcoffee/irmsd/tests/main.nf.test
./modules/nf-core/tcoffee/seqreformat/tests/main.nf.test
./modules/nf-core/tcoffee/tcs/tests/main.nf.test
./modules/nf-core/vcfanno/tests/main.nf.test
./subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test
./subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test
./subworkflows/nf-core/preprocess_rnaseq/tests/main.nf.test
./subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
./tests/modules/nf-core/angsd/contamination/main.nf
./tests/modules/nf-core/artic/minion/main.nf
./tests/modules/nf-core/authentict/deam2cont/main.nf
./tests/modules/nf-core/beagle5/beagle/main.nf
./tests/modules/nf-core/biscuit/epiread/main.nf
./tests/modules/nf-core/biscuit/vcf2bed/main.nf
./tests/modules/nf-core/calder2/main.nf
./tests/modules/nf-core/circexplorer2/annotate/main.nf
./tests/modules/nf-core/circexplorer2/parse/main.nf
./tests/modules/nf-core/clippy/main.nf
./tests/modules/nf-core/cooler/dump/main.nf
./tests/modules/nf-core/eido/convert/main.nf
./tests/modules/nf-core/eido/validate/main.nf
./tests/modules/nf-core/epang/place/main.nf
./tests/modules/nf-core/epang/split/main.nf
./tests/modules/nf-core/fqtk/main.nf
./tests/modules/nf-core/galah/main.nf
./tests/modules/nf-core/gamma/gamma/main.nf
./tests/modules/nf-core/gappa/examineassign/main.nf
./tests/modules/nf-core/gappa/examinegraft/main.nf
./tests/modules/nf-core/gappa/examineheattree/main.nf
./tests/modules/nf-core/gatk4/condensedepthevidence/main.nf
./tests/modules/nf-core/glimpse2/concordance/main.nf
./tests/modules/nf-core/goat/taxonsearch/main.nf
./tests/modules/nf-core/hapibd/main.nf
./tests/modules/nf-core/hicexplorer/hicpca/main.nf
./tests/modules/nf-core/hlala/typing/main.nf
./tests/modules/nf-core/hmmer/eslalimask/main.nf
./tests/modules/nf-core/hmmer/eslreformat/main.nf
./tests/modules/nf-core/hmmer/hmmalign/main.nf
./tests/modules/nf-core/hmmer/hmmbuild/main.nf
./tests/modules/nf-core/hmmer/hmmfetch/main.nf
./tests/modules/nf-core/ichorcna/createpon/main.nf
./tests/modules/nf-core/ichorcna/run/main.nf
./tests/modules/nf-core/icountmini/metagene/main.nf
./tests/modules/nf-core/icountmini/peaks/main.nf
./tests/modules/nf-core/icountmini/sigxls/main.nf
./tests/modules/nf-core/icountmini/summary/main.nf
./tests/modules/nf-core/ismapper/main.nf
./tests/modules/nf-core/krona/ktimporttext/main.nf
./tests/modules/nf-core/lissero/main.nf
./tests/modules/nf-core/megan/rma2info/main.nf
./tests/modules/nf-core/metaphlan/mergemetaphlantables/main.nf
./tests/modules/nf-core/metaphlan/metaphlan/main.nf
./tests/modules/nf-core/metaphlan3/mergemetaphlantables/main.nf
./tests/modules/nf-core/metaphlan3/metaphlan3/main.nf
./tests/modules/nf-core/miranda/main.nf
./tests/modules/nf-core/peka/main.nf
./tests/modules/nf-core/motus/downloaddb/main.nf
./tests/modules/nf-core/motus/merge/main.nf
./tests/modules/nf-core/motus/profile/main.nf
./tests/modules/nf-core/msisensor/msi/main.nf
./tests/modules/nf-core/msisensor2/msi/main.nf
./tests/modules/nf-core/nanolyse/main.nf
./tests/modules/nf-core/nanomonsv/parse/main.nf
./tests/modules/nf-core/pairix/main.nf
./tests/modules/nf-core/pints/caller/main.nf
./tests/modules/nf-core/plink/indep/main.nf
./tests/modules/nf-core/plink/indeppairwise/main.nf
./tests/modules/nf-core/qcat/main.nf
./tests/modules/nf-core/sam2lca/analyze/main.nf
./tests/modules/nf-core/scoary/main.nf
./tests/modules/nf-core/segemehl/align/main.nf
./tests/modules/nf-core/seroba/run/main.nf
./tests/modules/nf-core/sgdemux/main.nf
./tests/modules/nf-core/shapeit5/ligate/main.nf
./tests/modules/nf-core/shapeit5/phasecommon/main.nf
./tests/modules/nf-core/shapeit5/phaserare/main.nf
./tests/modules/nf-core/shapeit5/switch/main.nf
./tests/modules/nf-core/somalier/ancestry/main.nf
./tests/modules/nf-core/srst2/srst2/main.nf
./tests/modules/nf-core/svtk/baftest/main.nf
./tests/modules/nf-core/tailfindr/main.nf
./tests/modules/nf-core/ultraplex/main.nf
./tests/subworkflows/nf-core/bam_docounts_contamination_angsd/main.nf
./tests/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf
./tests/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
./tests/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
./tests/subworkflows/nf-core/vcf_impute_glimpse/main.nf
./tests/subworkflows/nf-core/vcf_phase_shapeit5/main.nf