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Merge pull request #269 from nf-core/reduce-full-test-output

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Deactivate saving of reads and other large files for full tests
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James A. Fellows Yates 2023-03-17 11:46:08 +01:00 committed by GitHub
commit af61e007b3
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1 changed files with 33 additions and 34 deletions
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67
conf/test_full.config
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@ -19,52 +19,51 @@ params {
// Genome references
hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
save_preprocessed_reads = true
save_preprocessed_reads = false
perform_shortread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = true
save_complexityfiltered_reads = true
perform_shortread_qc = true
shortread_qc_mergepairs = true
perform_shortread_complexityfilter = false
save_complexityfiltered_reads = false
perform_longread_qc = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
save_hostremoval_index = true
save_hostremoval_bam = true
save_hostremoval_unmapped = true
perform_longread_qc = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
save_hostremoval_index = false
save_hostremoval_bam = false
save_hostremoval_unmapped = false
perform_runmerging = true
save_runmerged_reads = true
perform_runmerging = true
save_runmerged_reads = false
run_centrifuge = true
centrifuge_save_reads = true
run_centrifuge = true
centrifuge_save_reads = false
run_diamond = true
run_diamond = true
run_kaiju = true
run_kaiju = true
run_kraken2 = true
kraken2_save_reads = true
kraken2_save_readclassification = true
kraken2_save_minimizers = true
run_kraken2 = true
kraken2_save_reads = false
kraken2_save_readclassification = false
kraken2_save_minimizers = false
run_krakenuniq = true
krakenuniq_save_reads = true
krakenuniq_save_readclassifications = true
run_krakenuniq = true
krakenuniq_save_reads = false
krakenuniq_save_readclassifications = false
run_bracken = true
run_bracken = true
run_malt = true
malt_save_reads = false
malt_generate_megansummary = true
run_malt = true
malt_save_reads = true
malt_generate_megansummary = true
run_metaphlan3 = true
run_metaphlan3 = true
run_motus = true
motus_save_mgc_read_counts = true
run_motus = true
motus_save_mgc_read_counts = true
run_profile_standardisation = true
run_krona = true
run_profile_standardisation = true
run_krona = true
}
cleanup = true