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Fix unite urls #766

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merged 16 commits into from
Jul 24, 2024
Merged

Fix unite urls #766

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e5e8f37
Work on SINTAX/UNITE dbs
erikrikarddaniel Jul 23, 2024
627fd8a
Merge branch 'dev' of github.com:nf-core/ampliseq into fix-unite-urls
erikrikarddaniel Jul 23, 2024
a6419ce
SINTAX/UNITE fixed urls
erikrikarddaniel Jul 23, 2024
be87d1b
Updated DADA UNITE urls
erikrikarddaniel Jul 23, 2024
68d9b29
New QIIME/UNITE urls
erikrikarddaniel Jul 24, 2024
2aae223
CHANGELOG.md
erikrikarddaniel Jul 24, 2024
79297b6
Fix duplicate filenames output from QIIME2_ANCOM_TAX
erikrikarddaniel Jul 24, 2024
d8a851f
Move table name
erikrikarddaniel Jul 24, 2024
21f6df8
More CHANGELOG.md
erikrikarddaniel Jul 24, 2024
9d11568
Fixed SINTAX/UNITE urls, tar -> fasta
erikrikarddaniel Jul 24, 2024
82a5665
Disable unite-fungi=9.0 -- seems broken at Unite
erikrikarddaniel Jul 24, 2024
5fde454
Warning in bin/taxref_reformat_sintax_tar.sh
erikrikarddaniel Jul 24, 2024
9a8094d
Revert most of the filename changes in QIIME2_ANCOM_TAX
erikrikarddaniel Jul 24, 2024
641fc4c
Disable Unite databases for --qiime_ref_taxonomy
erikrikarddaniel Jul 24, 2024
1d69762
prettier
erikrikarddaniel Jul 24, 2024
8e9b28d
[automated] Fix code linting
nf-core-bot Jul 24, 2024
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2 changes: 1 addition & 1 deletion modules/local/qiime2_ancom_tax.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ process QIIME2_ANCOM_TAX {
--to-tsv

if [ \$(grep -v '^#' -c ${table.baseName}-level-${taxlevel}.feature-table.tsv) -lt 2 ]; then
echo ${taxlevel} > ancom/\"WARNING Summing your data at taxonomic level ${taxlevel} produced less than two rows (taxa), ANCOM can't proceed -- did you specify a bad reference taxonomy?\".txt
echo ${taxlevel} > ancom/"${table.baseName}_WARNING_Summing_your_data_at_taxonomic_level_${taxlevel}_produced_less_than_two_rows_(taxa)_ANCOM_cant_proceed_--_did_you_specify_a_bad_reference_taxonomy.txt"
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Prepending ${table.baseName} unfortunately defeats its purpose, because the warning wont be picked up by

ampliseq/subworkflows/local/qiime2_ancom.nf

Line 45 in e66c9d3

QIIME2_ANCOM_TAX.out.ancom.subscribe { if ( it.baseName[0].toString().startsWith("WARNING") ) log.warn it.baseName[0].toString().replace("WARNING ","QIIME2_ANCOM_TAX: ") }
any more. Would need to be adjusted.

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Right, I'll put it after the WARNING.

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it.baseName[0].toString().replace("WARNING ","QIIME2_ANCOM_TAX: ") will still not work, because its now WARNING_ instead of WARNING (mind the space), correct? Other than that the PR seem fine to me.

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@erikrikarddaniel erikrikarddaniel Jul 24, 2024 •
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OK, I reverted most of this, just keeping the table.baseName in the filename. (I don't think we have a test case for this any more, since I corrected the Sintax urls.)

else
qiime composition add-pseudocount \\
--i-table lvl${taxlevel}-${table} \\
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