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q2pipe_step7_taxa_filtering.sh
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q2pipe_step7_taxa_filtering.sh
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#!/bin/bash
################################
# #
# Qiime 2 Pipeline #
# By: Patrick Gagne (NRCan) #
# Step 8 - Taxa Filtering #
# October 5, 2021 #
# #
################################
exit_on_error(){
echo "Qiime2 command error detected"
echo "Exiting program"
exit 1
}
optionfile=$1
if [ ! $optionfile ] || [ ! -e $optionfile ] || [ ! -r $optionfile ]
then
echo "ERROR: you must specify a valid, accessible qiime2 optionfile"
exit 1
fi
source $optionfile
if [ $TEMPORARY_DIRECTORY ]
then
echo "Overriding default temporary directory to $TEMPORARY_DIRECTORY"
if [ ! -d $TEMPORARY_DIRECTORY ] || [ ! -w $TEMPORARY_DIRECTORY ]
then
echo "ERROR: $TEMPORARY_DIRECTORY does not exist or is read only"
exit 2
fi
export TMPDIR=$TEMPORARY_DIRECTORY
fi
if [ ! $TMPDIR ]
then
export TMPDIR=/tmp
fi
if [ "$APPTAINER_COMMAND" != "" ]
then
echo "DEBUG: Checking temporary folder"
temp_check=$( $APPTAINER_COMMAND mktemp -t Q2PIPE_TEMPFOLDER_CHECK.XXXXXX.temp )
bname=$( basename $temp_check )
if [ ! -e $TMPDIR/$bname ]
then
echo "ERROR: Disparity between Apptainer temporary folder and system temporary folder"
echo "Please make sure both are pointing to the same folder"
exit 5
else
echo "DEBUG: Temporary file check status: OK"
rm $TMPDIR/Q2PIPE_TEMPFOLDER_CHECK.??????.temp
fi
fi
metatag="metafiltered_"
if [ "$p_where" == "" ]
then
echo "No metadata filtering parameter detected... skipping"
metatag=""
else
echo "Applying metadata filtering..."
echo "Metadata filtering parameter: $p_where"
$APPTAINER_COMMAND qiime feature-table filter-samples \
--i-table $ANALYSIS_NAME.table-dada2_dn"$p_perc_identity".qza \
--m-metadata-file $METADATA_FILE_PATH \
--p-where "$p_where" \
--o-filtered-table $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza || exit_on_error
$APPTAINER_COMMAND qiime feature-table summarize \
--i-table $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza \
--o-visualization $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qzv \
--m-sample-metadata-file $METADATA_FILE_PATH || exit_on_error
$APPTAINER_COMMAND qiime feature-table filter-seqs \
--i-data $ANALYSIS_NAME.rep-seqs-dada2_dn"$p_perc_identity".qza \
--i-table $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza \
--o-filtered-data $ANALYSIS_NAME."$metatag"rep-seqs-dada2_dn"$p_perc_identity".qza || exit_on_error
$APPTAINER_COMMAND qiime taxa barplot \
--i-table $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza \
--i-taxonomy $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $ANALYSIS_NAME."$metatag"barplots_taxo_dn"$p_perc_identity".qzv || exit_on_error
fi
#if [ "$SKIP_FILTERING" == "true" ]
#then
# echo "Skip filtering option detected, you must skip this step"
# #cp -v $ANALYSIS_NAME.table-dada2_dn"$p_perc_identity".qza $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza
# #cp -v $ANALYSIS_NAME.rep-seqs-dada2_dn"$p_perc_identity".qza $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza
# exit 0
#fi
taxa_filt=1
if [ ! $p_exclude ] && [ ! $p_include ]
then
echo "Both p_include and p_exclude are undefined, Taxa filtering will be skipped"
echo "table-dada2 and rep-seqs will copied as filtered_table for filename coherency"
cp -v $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza
cp -v $ANALYSIS_NAME."$metatag"rep-seqs-dada2_dn"$p_perc_identity".qza $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza
taxa_filt=0
fi
if [ $taxa_filt -eq 1 ]
then
if [ $p_exclude ]
then
excl_param="--p-exclude $p_exclude"
fi
if [ $p_include ]
then
excl_param="--p-include $p_include"
fi
if [ $p_exclude ] && [ $p_include ]
then
excl_param="--p-include $p_include --p-exclude $p_exclude"
fi
echo "Applying Taxa filtering..."
echo "Taxa filtering inclusion parameter: $p_include"
echo "Taxa filtering exclusion parameter: $p_exclude"
$APPTAINER_COMMAND qiime taxa filter-table \
--i-table $ANALYSIS_NAME."$metatag"table-dada2_dn"$p_perc_identity".qza \
--i-taxonomy $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
$excl_param \
--p-mode $p_mode \
--o-filtered-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza --verbose || exit_on_error
$APPTAINER_COMMAND qiime feature-table summarize \
--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
--o-visualization $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qzv --verbose \
--m-sample-metadata-file $METADATA_FILE_PATH
$APPTAINER_COMMAND qiime taxa filter-seqs \
--i-sequences $ANALYSIS_NAME."$metatag"rep-seqs-dada2_dn"$p_perc_identity".qza \
--i-taxonomy $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
$excl_param \
--p-mode $p_mode \
--o-filtered-sequences $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza --verbose || exit_on_error
$APPTAINER_COMMAND qiime feature-table tabulate-seqs \
--i-data $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza \
--o-visualization $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qzv --verbose
$APPTAINER_COMMAND qiime taxa barplot \
--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
--i-taxonomy $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
--m-metadata-file $METADATA_FILE_PATH \
--o-visualization $ANALYSIS_NAME.filtered_barplots_taxo_dn"$p_perc_identity".qzv --verbose || exit_on_error
fi
if [ "$GENERATE_PHYLOGENY" == "true" ]
then
echo "Generating phylogenetic trees"
$APPTAINER_COMMAND qiime phylogeny align-to-tree-mafft-fasttree \
--p-n-threads $NB_THREADS \
--i-sequences $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza \
--o-alignment $ANALYSIS_NAME.filtered_aligned_rep-seqs-dada2_dn"$p_perc_identity".qza \
--o-masked-alignment $ANALYSIS_NAME.filtered_masked_aligned_rep-seqs-dada2_dn"$p_perc_identity".qza \
--o-tree $ANALYSIS_NAME.unrooted_tree.qza \
--o-rooted-tree $ANALYSIS_NAME.rooted_tree.qza
fi