changed merged_bam output file name to sample_id.bam (#352)

* changed merged_bam output file name to sample_id.bam * changed optimus wdl file and changelog * Update Optimus.changelog.md * Update library/tasks/MergeSortBam.wdl Co-authored-by: Phil Shapiro <pshapiro@broadinstitute.org> Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> Co-authored-by: Phil Shapiro <pshapiro@broadinstitute.org>
HumanCellAtlas · Jun 10, 2020 · 94e459b · 94e459b
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commit 94e459b
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diff --git a/library/tasks/MergeSortBam.wdl b/library/tasks/MergeSortBam.wdl
@@ -4,6 +4,7 @@ task MergeSortBamFiles {
   input {
     Array[File] bam_inputs
     String sort_order
+    String output_bam_filename
 
     Int compression_level = 5
 
@@ -42,7 +43,7 @@ task MergeSortBamFiles {
       USE_THREADING=true \
       SORT_ORDER=${sort_order} \
       INPUT=${sep=' INPUT=' bam_inputs} \
-      OUTPUT=merged.bam \
+      OUTPUT=~{output_bam_filename} \
   }
 
   runtime {
@@ -53,6 +54,6 @@ task MergeSortBamFiles {
     preemptible: preemptible
   }
   output {
-    File output_bam = "merged.bam"
+    File output_bam = output_bam_filename
   }
 }
diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md
@@ -1,41 +1,34 @@
-#optimus_v3.0.0
-
-* Removed zarr formatted matrix and metrics outputs and replaced with loom
+# optimus_v3.0.0
+2020-06-10 (Date of Last Commit)
 
+* Removed zarr formatted matrix and metrics outputs and replaced with Loom
 * Removed emptyDrops for sn_rna mode
-
-* Loom file attribute names have changed: CellID: cell_names, Gene: gene_names and Accession: ensembl_ids
+* Updated Loom file attribute names: CellID to cell_names, Gene to gene_names, and Accession to ensembl_ids
+* Added metrics for mitochondrial reads
 
 # optimus_v2.0.0
+2020-02-08 (Date of Last Commit)
 
 * Fixed bug that resulted in emptyDrops output being incorrect
-
 * Updated workflow to WDL 1.0
 
 # optimus_v1.4.0
 
 2019-11-08 (Date of Last Commit)
 
 * Addition of support for V3 chemistry
-
 * Addition of input parameter validation step
-
 * Greatly improved documentation
-
 * Improvements to ZARR output
 
 # optimus_v1.3.6
 
 2019-09-23 (Date of Last Commit)
 
 * EmptyDrops output is now included in the ZARR output
-
 * The GTF modification step is removed from the scatter, resulting in better performance and caching
-
 * Memory of several tasks is increased
-
 * The ZARR output is now compulsory and the relevant input flag has been removed
-
 * Support for loom format has been added and a new optional flag dictates if the file is created
 Documentation has been updated
 
@@ -57,7 +50,6 @@ Documentation has been updated
 2019-08-08 (Date of Last Commit)
 
 * Release a new patch version of Optimus with an ambitious memory allocation for CalculateCellMetrics task.
-
 * This version and all future versions have been scientifically validated on Mouse reference version mm10 (GRCm39, Gencode M21)
 
 # optimus_v1.3.2

diff --git a/pipelines/optimus/Optimus.wdl b/pipelines/optimus/Optimus.wdl
@@ -222,6 +222,7 @@ workflow Optimus {
   call Merge.MergeSortBamFiles as MergeSorted {
     input:
       bam_inputs = PreMergeSort.bam_output,
+      output_bam_filename = sample_id + ".bam",
       sort_order = "coordinate"
   }