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Update Snakefile
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Revert snakefile prior to reftax.tsv edits
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@ksilnoaa
ksilnoaa authored Mar 28, 2024
1 parent aacfaab commit 8fa468f
Showing 1 changed file with 0 additions and 9 deletions.
9 changes: 0 additions & 9 deletions Snakefile
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Expand Up @@ -347,9 +347,6 @@ rule check_inputs_params_pe:
" echo 'OK: Reference sequences archive 01-imported/refseqs.qza found; reference sequences FASTA file 00-data/refseqs.fna not required.'; "
" elif [ -r '00-data/refseqs.fna' ]; then "
" echo 'OK: Reference sequences FASTA file 00-data/refseqs.fna found; it will be used to create reference sequences archive 01-imported/refseqs.qza.'; "
" qiime tools import --type 'FeatureData[Sequence]' --input-path 00-data/refseqs.fna --output-path 01-imported/refseqs.qza; "
" if [ -r '00-data/reftax.tsv' ]; then "
" qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path 00-data/reftax.tsv --output-path 01-imported/reftax.qza; "
" else echo 'Error: Reference sequences not found; either 01-imported/classifier.qza or 00-data/refseqs.fna or 01-imported/refseqs.qza is required.' && exit 1; "
" fi; "
"elif [ -r '01-imported/refseqs.qza' ]; then "
Expand All @@ -363,7 +360,6 @@ rule check_inputs_params_pe:
" echo 'OK: Reference taxonomy archive 01-imported/reftax.qza found; reference taxonomy file 00-data/reftax.tsv not required.'; "
" elif [ -r '00-data/reftax.tsv' ]; then "
" echo 'OK: Reference taxonomy file 00-data/reftax.tsv found; it will be used to create reference taxonomy archive 01-imported/reftax.qza.'; "
" qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path 00-data/reftax.tsv --output-path 01-imported/reftax.qza;"
" else echo 'Error: Reference taxonomy not found; either 00-data/reftax.tsv or 01-imported/reftax.qza is required.' && exit 1; "
" fi; "
"fi; "
Expand Down Expand Up @@ -397,24 +393,19 @@ rule check_inputs_params_se:
" echo 'OK: Reference sequences archive 01-imported/refseqs.qza found; reference sequences FASTA file 00-data/refseqs.fna not required.'; "
" elif [ -r '00-data/refseqs.fna' ]; then "
" echo 'OK: Reference sequences FASTA file 00-data/refseqs.fna found; it will be used to create reference sequences archive 01-imported/refseqs.qza.'; "
" qiime tools import --type 'FeatureData[Sequence]' --input-path 00-data/refseqs.fna --output-path 01-imported/refseqs.qza; "
" if [ -r '00-data/reftax.tsv' ]; then "
" qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path 00-data/reftax.tsv --output-path 01-imported/reftax.qza; "
" else echo 'Error: Reference sequences not found; either 01-imported/classifier.qza or 00-data/refseqs.fna or 01-imported/refseqs.qza is required.' && exit 1; "
" fi; "
"elif [ -r '01-imported/refseqs.qza' ]; then "
" echo 'OK: Reference sequences archive 01-imported/refseqs.qza found; reference sequences FASTA file 00-data/refseqs.fna not required.'; "
"elif [ -r '00-data/refseqs.fna' ]; then "
" echo 'OK: Reference sequences FASTA file 00-data/refseqs.fna found; it will be used to create reference sequences archive 01-imported/refseqs.qza.'; "
" qiime tools import --type 'FeatureData[Sequence]' --input-path 00-data/refseqs.fna --output-path 01-imported/refseqs.qza; "
"else echo 'Error: Reference sequences not found; either 00-data/refseqs.fna or 01-imported/refseqs.qza is required.' && exit 1; "
"fi; "
"if [ {params.classifymethod} != naive-bayes ]; then "
" if [ -r '01-imported/reftax.qza' ]; then "
" echo 'OK: Reference taxonomy archive 01-imported/reftax.qza found; reference taxonomy file 00-data/reftax.tsv not required.'; "
" elif [ -r '00-data/reftax.tsv' ]; then "
" echo 'OK: Reference taxonomy file 00-data/reftax.tsv found; it will be used to create reference taxonomy archive 01-imported/reftax.qza.'; "
" qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path 00-data/reftax.tsv --output-path 01-imported/reftax.qza;"
" else echo 'Error: Reference taxonomy not found; either 00-data/reftax.tsv or 01-imported/reftax.qza is required.' && exit 1; "
" fi; "
"fi; "
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