From 8fa468f0f1d10cadf662a766da78eb1c2d26a894 Mon Sep 17 00:00:00 2001
From: Katherine Silliman <124752903+ksilnoaa@users.noreply.github.com>
Date: Thu, 28 Mar 2024 13:44:16 -0400
Subject: [PATCH] Update Snakefile

Revert snakefile prior to reftax.tsv edits
---
 Snakefile | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/Snakefile b/Snakefile
index a245588..a3adeca 100644
--- a/Snakefile
+++ b/Snakefile
@@ -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 "
@@ -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; "
@@ -397,16 +393,12 @@ 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 "
@@ -414,7 +406,6 @@ rule check_inputs_params_se:
         "        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; "