sort bowtie2 outputs for reproducibility

chanzuckerberg · May 23, 2024 · 1bb6a26 · 1bb6a26
1 parent 29224db
commit 1bb6a26
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Showing 3 changed files with 20 additions and 1 deletion.
diff --git a/lib/idseq-dag/idseq_dag/steps/run_assembly.py b/lib/idseq-dag/idseq_dag/steps/run_assembly.py
@@ -221,6 +221,23 @@ def generate_read_to_contig_mapping(assembled_contig,
                 }
             )
         )
+
+        # sort bowtie2 output file
+        # samtools sort -n -O sam -o bowtie2.sam bowtie2.sam
+        samtools_sort_params = [
+            "sort",
+            "-n",
+            "-O", "sam",
+            "-o", output_bowtie_sam,
+            output_bowtie_sam
+        ]
+        command.execute(
+            command_patterns.SingleCommand(
+                cmd="samtools",
+                args=samtools_sort_params
+            )
+        )
+
         contig_stats, _ = generate_info_from_sam(output_bowtie_sam, read2contig, duplicate_cluster_sizes_path=duplicate_cluster_sizes_path)
         with open(output_contig_stats, 'w') as ocf:
             json.dump(contig_stats, ocf)

diff --git a/lib/idseq-dag/idseq_dag/util/m8.py b/lib/idseq-dag/idseq_dag/util/m8.py
@@ -431,7 +431,7 @@ def generate_taxon_count_json_from_m8(
                 agg_bucket["base_count"],
             }
             if agg_bucket.get('source_count_type'):
-                taxon_counts_row['source_count_type'] = list(agg_bucket['source_count_type'])
+                taxon_counts_row['source_count_type'] = sorted(list(agg_bucket['source_count_type']))
 
             taxon_counts_attributes.append(taxon_counts_row)
         output_dict = {

diff --git a/workflows/short-read-mngs/host_filter.wdl b/workflows/short-read-mngs/host_filter.wdl
@@ -276,6 +276,8 @@ task ercc_bowtie2_filter {
 
     ~{bowtie2_invocation}
 
+    samtools sort -n -O sam -o /tmp/bowtie2_ercc.sam /tmp/bowtie2_ercc.sam
+
     # Extract reads [pairs] that did NOT map to the index
     if [[ '~{paired}' == 'true' ]]; then
         #    1 (read paired)