Prepare for 1.4.0 release (#278)

* update optimus version
* Update README.md

Author: barkasn

pipelines/optimus/Optimus.wdl

@@ -20,7 +20,7 @@ workflow Optimus {
     description: "The optimus 3' pipeline processes 10x genomics sequencing data based on the v2 chemistry. It corrects cell barcodes and UMIs, aligns reads, marks duplicates, and returns data as alignments in BAM format and as counts in sparse matrix exchange format."
   }
   # version of this pipeline
-  String version = "optimus_v1.3.6"
+  String version = "optimus_v1.4.0"
 
   # Sequencing data inputs
   Array[File] r1_fastq

pipelines/optimus/README.md

@@ -79,7 +79,7 @@ The json file also contains metadata for the following reference information:
 * Annotations_gtf: a GTF containing gene annotations used for gene tagging (must match GTF in STAR reference)
 * Chemistry: an optional string description of whether data was generated with 10x V2 or V3 chemistry
   * Optional string: "tenX_v2" (default) or "tenX_v3"
-
+   * Note: Optimus validates this string. If the string does not match these options, the pipeline will fail. You can remove the checks by setting "force_no_check = true" in the input json.
 # Running Optimus
 
 * The [Optimus.wdl](https://github.com/HumanCellAtlas/skylab/blob/master/pipelines/optimus/Optimus.wdl) in the pipelines/optimus folder of the HCA skylab repository implements the workflow by importing individual modules ("tasks" written in  WDL script) from the skylab [Library](https://github.com/HumanCellAtlas/skylab/tree/master/library) folder.
@@ -153,14 +153,12 @@ The Optimus [Count](https://github.com/HumanCellAtlas/skylab/blob/master/library
 
 Empty droplets are lipid droplets that did not encapsulate a cell during 10x sequencing, but instead acquired cell-free RNA (secreted RNA or RNA released during cell lysis) from the solution in which the cells resided ([Lun, et al., 2018](https://www.ncbi.nlm.nih.gov/pubmed/?term=30902100). This ambient RNA can serve as a substrate for reverse transcription, leading to a small number of background reads. The Optimus pipeline calls the [RunEmptyDrops](https://github.com/HumanCellAtlas/skylab/blob/master/library/tasks/RunEmptyDrops.wdl) task which uses the [dropletUtils v.0.1.1](http://bioconductor.org/packages/release/bioc/html/DropletUtils.html) R package to flag cell barcodes that represent empty droplets rather than cells. A cell will be flagged if it contains fewer than 100 molecules. These metrics are stored in the output Zarr and [Loom](https://github.com/HumanCellAtlas/skylab/blob/master/pipelines/optimus/Loom_schema.md) files. 
 
-Boolean output_loom = false
-
 ### 9. Outputs
 
 Output files of the pipeline include:
 
 1. Cell x Gene unnormalized, but UMI-corrected, expression matrices
-2. Unfiltered, sorted BAM file with barcode and downstream analysis [Tags](Bam_tags.md)
+2. Unfiltered, sorted BAM file with barcode and downstream analysis [tags](Bam_tags.md)
 3. Cell metadata, including cell metrics
 4. Gene metadata, including gene metrics
 
@@ -177,9 +175,12 @@ Following are the types of files produced from the pipeline.
 | zarr_output_files | {unique_id}.zarr!.zattrs | Zarr | Array | 
 | loom_output_file | output.loom | Loom | Loom | Loom file with expression data and metadata | N/A |
 
+
+The Zarr array is the default output. The Zarr schema version is detailed in the array as 'optimus_output_schema_version'. The schema version is specified to the Zarr using the [create_zarr_optimus.py](https://github.com/HumanCellAtlas/skylab/blob/master/docker/zarr-output/create_zarr_optimus.py) script. 
+
 The Loom file is an optional output that is specified in the "meta" section of the [Optimus workflow](https://github.com/HumanCellAtlas/skylab/blob/master/pipelines/optimus/Optimus.wdl) with the following boolean command:
 
-"Boolean output_loom = false"
+> "Boolean output_loom = false"
 
 To obtain a Loom file, the boolean parameter "false" must be changed to "true".