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add smaller test database
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d4straub committed Mar 8, 2024

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1 parent 1617780 commit f68b18a
Showing 5 changed files with 30 additions and 11 deletions.
14 changes: 8 additions & 6 deletions bin/taxref_reformat_sidle.sh
Original file line number Diff line number Diff line change
@@ -1,19 +1,21 @@
#!/bin/sh

derep="$1"

# Untar any tar file in the working directory
tar xzf database.tar.gz

# Greengenes 13_8
if [ -d "gg_13_8_otus" ]; then
mv gg_13_8_otus/rep_set/99_otus.fasta gg_13_8_otus_rep_set_99_otus.seq.fasta
mv gg_13_8_otus/rep_set_aligned/99_otus.fasta gg_13_8_otus_rep_set_aligned_99_otus.alnseq.fasta
mv gg_13_8_otus/taxonomy/99_otu_taxonomy.txt gg_13_8_otus_taxonomy_99_otu_taxonomy.tax.txt
mv gg_13_8_otus/rep_set/${derep}_otus.fasta gg_13_8_otus_rep_set_${derep}_otus.seq.fasta
mv gg_13_8_otus/rep_set_aligned/${derep}_otus.fasta gg_13_8_otus_rep_set_aligned_${derep}_otus.alnseq.fasta
mv gg_13_8_otus/taxonomy/${derep}_otu_taxonomy.txt gg_13_8_otus_taxonomy_${derep}_otu_taxonomy.tax.txt
# remove uncompressed folder
rm -r gg_13_8_otus
elif [ -d "SILVA_128_QIIME_release" ]; then
mv SILVA_128_QIIME_release/rep_set/rep_set_all/99/99_otus.fasta SILVA_128_QIIME_release_rep_set_all_99_otus.seq.fasta
gunzip -c /SILVA_128_QIIME_release/rep_set_aligned/99/99_otus_aligned.fasta.gz > SILVA_128_QIIME_release_rep_set_aligned_99_otus_aligned.alnseq.fasta
mv SILVA_128_QIIME_release/taxonomy/taxonomy_all/99/consensus_taxonomy_7_levels SILVA_128_QIIME_release_taxonomy_all_99_consensus_taxonomy_7_levels.tax.txt
mv SILVA_128_QIIME_release/rep_set/rep_set_all/${derep}/${derep}_otus.fasta SILVA_128_QIIME_release_rep_set_all_${derep}_otus.seq.fasta
gunzip -c /SILVA_128_QIIME_release/rep_set_aligned/${derep}/${derep}_otus_aligned.fasta.gz > SILVA_128_QIIME_release_rep_set_aligned_${derep}_otus_aligned.alnseq.fasta
mv SILVA_128_QIIME_release/taxonomy/taxonomy_all/${derep}/consensus_taxonomy_7_levels SILVA_128_QIIME_release_taxonomy_all_${derep}_consensus_taxonomy_7_levels.tax.txt
# remove uncompressed folder
rm -r SILVA_128_QIIME_release
else
9 changes: 9 additions & 0 deletions conf/ref_databases.config
Original file line number Diff line number Diff line change
@@ -524,5 +524,14 @@ params {
fmtscript = "taxref_reformat_sidle.sh"
taxlevels = "D,P,C,O,F,G,S"
}
'greengenes88' {
title = "Greengenes - Version 13_8 - clustered at 88% similarity - for testing purposes only"
file = [ "ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz" ]
tree_qza = [ "https://data.qiime2.org/2021.4/common/sepp-refs-gg-13-8.qza" ]
citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139"
fmtscript = "taxref_reformat_sidle.sh"
taxlevels = "D,P,C,O,F,G,S"
derep = "88"
}
}
}
7 changes: 4 additions & 3 deletions conf/test_multiregion.config
Original file line number Diff line number Diff line change
@@ -23,11 +23,12 @@ params {
input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/samplesheet_multiregion.tsv"
metadata = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/metadata_multiregion.tsv"
input_multiregion = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/regions_multiregion.tsv"
sidle_ref_taxonomy = "greengenes"
sidle_ref_taxonomy = "greengenes88"

// Prevent default taxonomic classification
skip_dada_taxonomy = true

//restrict ANCOM analysis to higher taxonomic levels
tax_agglom_max = 4
// Reduce runtimes
skip_alpha_rarefaction = true
tax_agglom_max = 3
}
3 changes: 2 additions & 1 deletion modules/local/format_taxonomy_sidle.nf
Original file line number Diff line number Diff line change
@@ -21,8 +21,9 @@ process FORMAT_TAXONOMY_SIDLE {
task.ext.when == null || task.ext.when

script:
def derep = params.sidle_ref_databases[params.sidle_ref_taxonomy]["derep"] ?: "99"
"""
${params.sidle_ref_databases[params.sidle_ref_taxonomy]["fmtscript"]}
${params.sidle_ref_databases[params.sidle_ref_taxonomy]["fmtscript"]} ${derep}
#Giving out information
echo -e "--sidle_ref_taxonomy: ${params.sidle_ref_taxonomy}\n" >ref_taxonomy.${suffix}.txt
8 changes: 7 additions & 1 deletion nextflow_schema.json
Original file line number Diff line number Diff line change
@@ -508,7 +508,13 @@
"type": "string",
"help_text": "",
"description": "Name of supported database, and optionally also version number",
"enum": ["silva", "silva=128", "greengenes", "greengenes=13_8"]
"enum": [
"silva",
"silva=128",
"greengenes",
"greengenes=13_8",
"greengenes88"
]
},
"sidle_ref_tax_custom": {
"type": "string",

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