update docs for snippy streamline and snippy tree.md

docs/workflows/phylogenetic_construction/snippy_streamline.md

@@ -188,6 +188,7 @@ For all cases:
 | snippy_centroid_version | String | Centroid version used |
 | snippy_cg_snp_matrix | File | CSV file of core genome pairwise SNP distances between samples, calculated from the final alignment  |
 | snippy_concatenated_variants | File | The concatenated variants file |
+| snippy_combined_qc_metrics | File | Combined QC metrics file containing concatenated QC metrics from all samples. The file is a tab-separated values (TSV) file with the following columns:<br>- samplename<br>- reads_aligned_to_reference<br>- total_reads<br>- percent_reads_aligned<br>- variants_total<br>- percent_ref_coverage<br>- #rname<br>- startpos<br>- endpos<br>- numreads<br>- covbases<br>- coverage<br>- meandepth<br>- meanbaseq<br>- meanmapq<br><br>The last set of columns (`#rname` to `meanmapq`) may repeat for each chromosome or contig in the reference genome. |
 | snippy_filtered_metadata | File | TSV recording the columns of the Terra data table that were used in the summarize_data task |
 | snippy_final_alignment | File | Final alignment (FASTA file) used to generate the tree (either after snippy alignment, gubbins recombination removal, and/or core site selection with SNP-sites) |
 | snippy_final_tree | File | Final phylogenetic tree produced by Snippy_Streamline |

docs/workflows/phylogenetic_construction/snippy_tree.md

@@ -312,6 +312,7 @@ Sequencing data used in the Snippy_Tree workflow must:
 |---|---|---|
 | snippy_cg_snp_matrix | File | CSV file of core genome pairwise SNP distances between samples, calculated from the final alignment  |
 | snippy_concatenated_variants | File | Concatenated snippy_results file across all samples in the set |
+| snippy_combined_qc_metrics | File | Combined QC metrics file containing concatenated QC metrics from all samples. The file is a tab-separated values (TSV) file with the following columns:<br>- samplename<br>- reads_aligned_to_reference<br>- total_reads<br>- percent_reads_aligned<br>- variants_total<br>- percent_ref_coverage<br>- #rname<br>- startpos<br>- endpos<br>- numreads<br>- covbases<br>- coverage<br>- meandepth<br>- meanbaseq<br>- meanmapq<br><br>The last set of columns (`#rname` to `meanmapq`) may repeat for each chromosome or contig in the reference genome. |
 | snippy_filtered_metadata | File | TSV recording the columns of the Terra data table that were used in the summarize_data task |
 | snippy_final_alignment | File | Final alignment (FASTA file) used to generate the tree (either after snippy alignment, gubbins recombination removal, and/or core site selection with SNP-sites) |
 | snippy_final_tree | File | Newick tree produced from the final alignment. Depending on user input for core_genome, the tree could be a core genome tree (default when core_genome is true) or whole genome tree (if core_genome is false) |

workflows/phylogenetics/wf_snippy_tree.wdl

@@ -184,14 +184,14 @@ workflow snippy_tree_wf {
     call shared_variants_task.shared_variants {
       input:
         concatenated_variants = concatenate_variants.concatenated_variants, 
-        concatenated_file_name = tree_name_updated + "_combined_qc_metrics.tsv",
+        concatenated_file_name = tree_name_updated
     }
   }
   if (defined(snippy_variants_qc_metrics)) {
     call file_handling.cat_files as concatenate_qc_metrics {
       input:
         files_to_cat = select_first([snippy_variants_qc_metrics]),
-        concatenated_file_name = tree_name_updated,
+        concatenated_file_name = tree_name_updated + "_combined_qc_metrics.tsv"
         skip_extra_headers = true
     }
   }