fix building phylo tree

mmeds/snakemake/rules/process_sequencing_data.smk

@@ -70,15 +70,18 @@ rule build_phylogenetic_tree:
         feature_table = "tables/asv_table.qza",
         rep_seqs = "tables/rep_seqs_table.qza"
     output:
+        alignment = temp("tables/alignment.qza")
+        masked_alignment = temp("tables/masked_alignment.qza")
+        unrooted_tree = temp("tables/unrooted_tree.qza")
         feature_table_viz = "tables/asv_table_viz.qzv",
         rooted_tree = "tables/rooted_tree.qza"
     conda:
         "qiime2-2020.8.0"
     shell:
         """
         qiime feature-table summarize --i-table {input.feature_table} --o-visualization {output.feature_table_viz}
-        qiime alignment mafft --i-sequences {input.rep_seqs} --o-alignment temp_files/alignment.qza
-        qiime alignment mask --i-alignment temp_files/alignment.qza --o-masked-alignment temp_files/masked_alignment.qza
-        qiime phylogeny fasttree --i-alignment temp_files/masked_alignment.qza --o-tree temp_files/unrooted_tree.qza
-        qiime phylogeny midpoint-root --i-tree temp_files/unrooted_tree.qza --o-rooted-tree tables/rooted_tree.qza
+        qiime alignment mafft --i-sequences {input.rep_seqs} --o-alignment {output.alignment}
+        qiime alignment mask --i-alignment {output.alignment} --o-masked-alignment {output.masked_alignment}
+        qiime phylogeny fasttree --i-alignment {output.masked_alignment} --o-tree {output.unrooted_tree}
+        qiime phylogeny midpoint-root --i-tree {output.unrooted_tree} --o-rooted-tree {output.rooted_tree}
         """