diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_bams_wf.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_bams_wf.cwl
index 77743a6..3b1ab51 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_bams_wf.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_bams_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     Compare 2 input BAM files and report results.
     Exit 0 if sucess.
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_md5_wf.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_md5_wf.cwl
index 471900b..e4a00bc 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_md5_wf.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/check_md5_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     Calculates the MD5 hash of the input file and compares it to the input MD5 hash.
     If hashes match: Exit 0
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/calc_md5.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/calc_md5.cwl
index 9d2a724..e72cf7c 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/calc_md5.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/calc_md5.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     Calculate the MD5 hash for the input file.
 
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/compare_bams.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/compare_bams.cwl
index c65ba33..afa8ff3 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/compare_bams.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/compare_bams.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     Compare 2 input BAM files using [BamUtil diff](https://genome.sph.umich.edu/wiki/BamUtil:_diff)
 
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/read_file.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/read_file.cwl
index d453a93..c24f2df 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/read_file.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/read_file.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: ExpressionTool
 
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/string_comparison.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/string_comparison.cwl
index 7420cf0..88b8a02 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/string_comparison.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/string_comparison.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: []
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/untar_dir.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/untar_dir.cwl
index d5ad119..e4d50b8 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/untar_dir.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/components/untar_dir.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     Extract all files from archive.tar and filter through gzip
 
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker-tar.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker-tar.cwl
index ff3d050..32626ba 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker-tar.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker-tar.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A workflow to verify the proper execution of [TOPMed RNA-seq Workflow](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl)
 
@@ -20,20 +21,16 @@ inputs:
     type: File[]
   prefix_str:
     type: string
-  threads:
-    type: int
-  memory:
-    type: int
   rsem_ref_dir_tar:
     type: File
   max_frag_len:
     type: int
   estimate_rspd:
-    type: string
+    type: boolean
   is_stranded:
-    type: string
+    type: boolean
   paired_end:
-    type: string
+    type: boolean
   genes_gtf:
     type: File
   genome_fasta:
@@ -41,8 +38,6 @@ inputs:
     secondaryFiles:
       - .fai
       - ^.dict
-  java_path:
-    type: string
   rnaseqc_flags:
     type: string[]
   # gatk_flags:
@@ -72,8 +67,6 @@ inputs:
   #   type: string
   # hash_exon_counts:
   #   type: string
-  hash_count_metrics:
-    type: string
   # hash_count_outputs:
   #   type: string
   checker_star_output_bam:
@@ -157,8 +150,6 @@ steps:
       star_index: untar_star_index/untarred_dir
       fastqs: fastqs
       prefix_str: prefix_str
-      threads: threads
-      memory: memory
       rsem_ref_dir: untar_rsem_reference/untarred_dir
       max_frag_len: max_frag_len
       estimate_rspd: estimate_rspd
@@ -166,7 +157,6 @@ steps:
       paired_end: paired_end
       genes_gtf: genes_gtf
       genome_fasta: genome_fasta
-      java_path: java_path
       rnaseqc_flags: rnaseqc_flags
       # gatk_flags: gatk_flags
     out:
@@ -310,7 +300,7 @@ steps:
   #   out: [out_hash_string]
 
 $namespaces:
-  s: https://schema.org/
+  s: http://schema.org/
 
 $schemas:
 - http://dublincore.org/2012/06/14/dcterms.rdf
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker.cwl
index 53a1989..718247b 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/checker-workflows/rnaseq_pipeline_fastq_checker.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A workflow to verify the proper execution of [TOPMed RNA-seq Workflow](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl)
 
@@ -18,20 +19,16 @@ inputs:
     type: File[]
   prefix_str:
     type: string
-  threads:
-    type: int
-  memory:
-    type: int
   rsem_ref_dir:
     type: Directory
   max_frag_len:
     type: int
   estimate_rspd:
-    type: string
+    type: boolean
   is_stranded:
-    type: string
+    type: boolean
   paired_end:
-    type: string
+    type: boolean
   genes_gtf:
     type: File
   genome_fasta:
@@ -39,8 +36,6 @@ inputs:
     secondaryFiles:
       - .fai
       - ^.dict
-  java_path:
-    type: string
   rnaseqc_flags:
     type: string[]
   # gatk_flags:
@@ -70,8 +65,6 @@ inputs:
   #   type: string
   # hash_exon_counts:
   #   type: string
-  hash_count_metrics:
-    type: string
   # hash_count_outputs:
   #   type: string
   checker_star_output_bam:
@@ -143,8 +136,6 @@ steps:
       star_index: star_index
       fastqs: fastqs
       prefix_str: prefix_str
-      threads: threads
-      memory: memory
       rsem_ref_dir: rsem_ref_dir
       max_frag_len: max_frag_len
       estimate_rspd: estimate_rspd
@@ -152,7 +143,6 @@ steps:
       paired_end: paired_end
       genes_gtf: genes_gtf
       genome_fasta: genome_fasta
-      java_path: java_path
       rnaseqc_flags: rnaseqc_flags
       # gatk_flags: gatk_flags
     out:
@@ -296,7 +286,7 @@ steps:
   #   out: [out_hash_string]
 
 $namespaces:
-  s: https://schema.org/
+  s: http://schema.org/
 
 $schemas:
 - http://dublincore.org/2012/06/14/dcterms.rdf
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/indexbam.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/indexbam.cwl
index beb4be4..1451c81 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/indexbam.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/indexbam.cwl
@@ -1,25 +1,25 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A wrapper for running `samtools index <bam>`.
 
 cwlVersion: v1.0
 class: CommandLineTool
-id: "run-index-bam"
 label: "run-index-bam"
-baseCommand: ["samtools", "index"]
+baseCommand: [ samtools, index ]
 
 requirements:
-- class: InlineJavascriptRequirement
-- class: DockerRequirement
-  dockerPull: heliumdatacommons/topmed-rnaseq:latest
-- class: InitialWorkDirRequirement
-  listing:
-    - $(inputs.input_bam)
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/samtools:1.8--4
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.input_bam)
 
 inputs:
   input_bam:
     type: File
     inputBinding:
       position: 1
+      valueFrom: $(self.basename)
 
 outputs:
   bam_index:
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml b/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml
index 967e8e9..e6d6b22 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml
@@ -11,9 +11,9 @@ rsem_ref_dir:
     class: Directory
     location: /rsem_ref/
 max_frag_len: 1000
-estimate_rspd: "true"
-is_stranded: "true"
-paired_end: "true"
+estimate_rspd: true
+is_stranded: true
+paired_end: true
 genes_gtf: {
     class: File,
     path: gencode.v26.annotation.withTranscriptID.gtf
@@ -22,9 +22,6 @@ genome_fasta: {
     class: File,
     path: Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta
 }
-java_path: /usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java
-memory: 8
 rnaseqc_flags: ["noDoC", "strictMode"]
 # gatk_flags: []
 prefix_str: "LC_C13_cRNA"
-threads: 4
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rsem-example.yml b/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rsem-example.yml
index fab64df..73fa82b 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rsem-example.yml
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rsem-example.yml
@@ -7,7 +7,7 @@ transcriptome_bam: {
 }
 prefix_str: "LC_C13_cRNA"
 max_frag_len: 1000
-estimate_rspd: "true"
-is_stranded: "true"
-paired_end: "true"
+estimate_rspd: true
+is_stranded: true
+paired_end: true
 threads: 4
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl
index c31c9d6..60086b5 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A CWL wrapper for [run_MarkDuplicates.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_MarkDuplicates.py)
 
@@ -9,35 +10,42 @@ doc: |
 
 cwlVersion: v1.0
 class: CommandLineTool
-id: "run-MarkDuplicates"
 label: "run-MarkDuplicates"
-baseCommand: ["python3", "-u", "/src/run_MarkDuplicates.py"]
+baseCommand: [java]
 
-requirements:
-  - class: DockerRequirement
-    dockerPull: heliumdatacommons/topmed-rnaseq:latest
+requirements: # turn back into a hint when the biocontainer has its classpath
+              #   updated
+  EnvVarRequirement:
+    envDef:
+      CLASSPATH: /usr/local/share/picard-2.9.2-2/picard.jar
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/picard:2.9.2--2
 
 inputs:
   input_bam:
     type: File
-    inputBinding:
-      position: 1
   prefix_str:
     type: string
-    inputBinding:
-      position: 2
-  memory:
-    type: int
-    inputBinding:
-      position: 3
-      prefix: --memory
+
+arguments:
+  - prefix: -Xmx
+    valueFrom: $(runtime.ram)M
+    separate: false
+  - picard.cmdline.PicardCommandLine
+  - MarkDuplicates
+  - I=$(inputs.input_bam.path)
+  - O=$(runtime.outdir)/$(inputs.input_bam.nameroot).md.bam
+  - M=$(runtime.outdir)/$(inputs.prefix_str).marked_dup_metrics.txt
+  - ASSUME_SORT_ORDER=coordinate
+  - OPTICAL_DUPLICATE_PIXEL_DISTANCE=100
 
 outputs:
   bam_file:
     type: File
     outputBinding:
-      glob: "*.md.bam"
+      glob: $(inputs.input_bam.nameroot).md.bam
   metrics:
     type: File
     outputBinding:
-      glob: "*.marked_dup_metrics.txt"
+      glob: $(inputs.prefix_str).marked_dup_metrics.txt
+
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/rna_seqc.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/rna_seqc.cwl
index 7d09bf9..206536d 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/rna_seqc.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/rna_seqc.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A CWL wrapper for [run_rnaseqc.py](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/src/run_rnaseqc.py) duplicated from [run_rnaseqc.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_rnaseqc.py) with minor modifications.
 
@@ -9,12 +10,12 @@ doc: |
 
 cwlVersion: v1.0
 class: CommandLineTool
-id: "run-seqc"
 label: "run-seqc"
 # run_rnaseqc.py is not an executable file in the docker container.
 baseCommand: ["python3", "/src/run_rnaseqc.py"]
 
 requirements:
+  InlineJavascriptRequirement: {}
   DockerRequirement:
     dockerPull: heliumdatacommons/topmed-rnaseq:latest
 
@@ -40,16 +41,6 @@ inputs:
     type: string
     inputBinding:
       position: 4
-  java_path:
-    type: string
-    inputBinding:
-      position: 5
-      prefix: --java
-  memory:
-    type: int
-    inputBinding:
-      position: 6
-      prefix: --memory
   rnaseqc_flags:
     type:
       type: array
@@ -70,6 +61,11 @@ inputs:
   #     position: 8
   #     prefix: --gatk_flags
 
+arguments:
+  - prefix: --memory
+    valueFrom: $(runtime.ram / 1024)
+  - prefix: --java
+    valueFrom: /usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java
 outputs:
   gene_rpkm:
     type: File
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl
index 589cd2e..3f7bbf0 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md).
     Example input files: [Dockstore.json](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml).
@@ -15,15 +16,16 @@ doc: |
 
 cwlVersion: v1.0
 class: Workflow
-id: "TOPMed_RNA-seq"
 label: "TOPMed_RNA-seq"
 
 requirements:
-  - class: SubworkflowFeatureRequirement
-  - class: ResourceRequirement
-    coresMin: 4
-    ramMin: 16
-    tmpdirMin: 51200
+  SubworkflowFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+# hints:
+#   ResourceRequirement:
+#     coresMin: 4
+#     ramMin: 16
+#     #tmpdirMin: 51200
 
 inputs:
   star_index:
@@ -32,20 +34,16 @@ inputs:
     type: File[]
   prefix_str:
     type: string
-  threads:
-    type: int
-  memory:
-    type: int
   rsem_ref_dir:
     type: Directory
   max_frag_len:
     type: int
   estimate_rspd:
-    type: string
+    type: boolean
   is_stranded:
-    type: string
+    type: boolean
   paired_end:
-    type: string
+    type: boolean
   genes_gtf:
     type: File
   genome_fasta:
@@ -53,8 +51,6 @@ inputs:
     secondaryFiles:
       - .fai
       - ^.dict
-  java_path:
-    type: string
   rnaseqc_flags:
     type: string[]
   # gatk_flags:
@@ -64,100 +60,123 @@ inputs:
   #     items: string
 
 outputs:
-  - id: star_output_bam
-    outputSource: run_star/bam_file
+  star_output_bam:
+    outputSource: sort_bam/output_file
     type: File
-  - id: star_output_bam_index
-    outputSource: run_star/bam_index
+  star_output_bam_index:
+    outputSource: index_bam/bam_index
     type: File
-  - id: star_output_transcriptome_bam
+  star_output_transcriptome_bam:
     outputSource: run_star/transcriptome_bam
     type: File
-  - id: star_output_chimeric_junctions
+  star_output_chimeric_junctions:
     outputSource: run_star/chimeric_junctions
     type: File
-  - id: star_output_chimeric_bam_file
-    outputSource: run_star/chimeric_bam_file
+  star_output_chimeric_bam_file:
+    outputSource: sort_chimeras/output_file
     type: File
-  - id: star_output_chimeric_bam_index
-    outputSource: run_star/chimeric_bam_index
+  star_output_chimeric_bam_index:
+    outputSource: index_chimeras/bam_index
     type: File
-  - id: star_output_read_counts
+  star_output_read_counts:
     outputSource: run_star/read_counts
     type: File
-  - id: star_output_junctions
+  star_output_junctions:
     outputSource: run_star/junctions
     type: File
-  - id: star_output_junctions_pass1
+  star_output_junctions_pass1:
     outputSource: run_star/junctions_pass1
     type: File
-  - id: star_output_logs
+  star_output_logs:
     outputSource: run_star/logs
     type: File[]
-  - id: markduplicates_output_bam
+  markduplicates_output_bam:
     outputSource: run_markduplicates/bam_file
     type: File
-  - id: markduplicates_output_metrics
+  markduplicates_output_metrics:
     outputSource: run_markduplicates/metrics
     type: File
-  - id: markduplicates_bam_index
+  markduplicates_bam_index:
     outputSource: run_index_markduplicates_bam/bam_index
     type: File
-  - id: rsem_output_gene_results
+  rsem_output_gene_results:
     outputSource: run_rsem/gene_results
     type: File
-  - id: rsem_output_isoforms_results
+  rsem_output_isoforms_results:
     outputSource: run_rsem/isoforms_results
     type: File
-  - id: rna-seqc_output_gene_rpkm
+  rna-seqc_output_gene_rpkm:
     outputSource: run_rna-seqc/gene_rpkm
     type: File
-  - id: rna-seqc_output_gene_counts
+  rna-seqc_output_gene_counts:
     outputSource: run_rna-seqc/gene_counts
     type: File
-  - id: rna-seqc_output_exon_counts
+  rna-seqc_output_exon_counts:
     outputSource: run_rna-seqc/exon_counts
     type: File
-  - id: rna-seqc_output_count_metrics
+  rna-seqc_output_count_metrics:
     outputSource: run_rna-seqc/count_metrics
     type: File
-  - id: rna-seqc_output_count_outputs
+  rna-seqc_output_count_outputs:
     outputSource: run_rna-seqc/count_outputs
     type: File
 
 steps:
   run_star:
-    requirements:
-      ResourceRequirement:
-        coresMin: 4
-        ramMin: 16
-        tmpdirMin: 51200
     run: star.cwl
     in:
       star_index: star_index
       fastqs: fastqs
-      prefix_str: prefix_str
-      threads: threads
+      prefix: prefix_str
     out:
       [
-        bam_file,
-        bam_index,
+        bam,
         transcriptome_bam,
         chimeric_junctions,
-        chimeric_bam_file,
-        chimeric_bam_index,
+        chimeric_bam,
         read_counts,
         junctions,
         junctions_pass1,
         logs
       ]
 
+  sort_bam:
+    run: samtools-sort.cwl
+    in:
+      input:
+        source: run_star/bam
+      output_name:
+        source: prefix_str
+        valueFrom: $(self).Aligned.sortedByCoord.out.bam
+    out: [ output_file ]
+
+  sort_chimeras:
+    run: samtools-sort.cwl
+    in:
+      input:
+        source: run_star/chimeric_bam
+      output_name:
+        source: prefix_str
+        valueFrom: $(self).Chimeric.out.sorted.bam
+    out: [ output_file ]
+
+  index_bam:
+    run: indexbam.cwl
+    in:
+      input_bam: sort_bam/output_file
+    out: [bam_index]
+
+  index_chimeras:
+    run: indexbam.cwl
+    in:
+      input_bam: sort_chimeras/output_file
+    out: [bam_index]
+
   run_markduplicates:
     run: markduplicates.cwl
     in:
-      input_bam: run_star/bam_file
+      input_bam: sort_bam/output_file
       prefix_str: prefix_str
-      memory: memory
     out:
       [
         bam_file,
@@ -180,7 +199,6 @@ steps:
       estimate_rspd: estimate_rspd
       is_stranded: is_stranded
       paired_end: paired_end
-      threads: threads
     out:
       [
         gene_results,
@@ -194,8 +212,6 @@ steps:
       genes_gtf: genes_gtf
       genome_fasta: genome_fasta
       prefix_str: prefix_str
-      java_path: java_path
-      memory: memory
       rnaseqc_flags: rnaseqc_flags
       # gatk_flags: gatk_flags
     out:
@@ -208,7 +224,7 @@ steps:
       ]
 
 $namespaces:
-  s: https://schema.org/
+  s: http://schema.org/
 
 $schemas:
 - http://dublincore.org/2012/06/14/dcterms.rdf
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/rsem.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/rsem.cwl
index 5de090a..514dad9 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/rsem.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/rsem.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A CWL wrapper for [run_RSEM.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_RSEM.py)
 
@@ -7,61 +8,64 @@ doc: |
 
 cwlVersion: v1.0
 class: CommandLineTool
-id: "run-rsem"
 label: "run-rsem"
-baseCommand: /src/run_RSEM.py
+baseCommand: rsem-calculate-expression
 
 requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.rsem_ref_dir)
+        writable: true
+hints:
   DockerRequirement:
-    dockerPull: heliumdatacommons/topmed-rnaseq:latest
+    dockerPull: quay.io/biocontainers/rsem:1.3.0--boost1.64_3
 
 inputs:
   rsem_ref_dir:
     type: Directory
-    default:
-      type: Directory
     inputBinding:
-      position: 1
+      position: 2
+      valueFrom: $(self.basename)/rsem_reference
   transcriptome_bam:
     type: File
     inputBinding:
-      position: 2
+      position: 1
   prefix_str:
     type: string
     inputBinding:
       position: 3
+      valueFrom: $(self).rsem
   max_frag_len:
     type: int
     inputBinding:
-      position: 4
-      prefix: --max_frag_len
+      prefix: --fragment-length-max
   estimate_rspd:
-    type: string
+    type: boolean
     inputBinding:
-      position: 5
-      prefix: --estimate_rspd
+      prefix: --estimate-rspd
   is_stranded:
-    type: string
-    inputBinding:
-      position: 6
-      prefix: --is_stranded
+    type: boolean
   paired_end:
-    type: string
+    type: boolean
     inputBinding:
-      position: 7
-      prefix: --paired_end
-  threads:
-    type: int
-    inputBinding:
-      position: 8
-      prefix: --threads
+      prefix: --paired-end
+
+arguments:
+  - prefix: --num-threads
+    valueFrom: $(runtime.cores)
+  - prefix: --fragment-length-max
+    valueFrom: "1000"
+  - --no-bam-output
+  - --bam
+  - ${if (inputs.is_stranded) { return ["--forward-prob", "0.0"];} }
 
 outputs:
   gene_results:
     type: File
     outputBinding:
-      glob: "*.rsem.genes.results"
+      glob: $(inputs.prefix_str).rsem.genes.results
   isoforms_results:
     type: File
     outputBinding:
-      glob: "*.rsem.isoforms.results"
+      glob: $(inputs.prefix_str).rsem.isoforms.results
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/samtools-sort.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/samtools-sort.cwl
new file mode 100644
index 0000000..887518d
--- /dev/null
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/samtools-sort.cwl
@@ -0,0 +1,88 @@
+#!/usr/bin/env cwl-runner
+
+# adapted from https://github.com/common-workflow-language/workflows/tree/master/tools
+
+class: CommandLineTool
+
+$namespaces:
+  dct: http://purl.org/dc/terms/
+$schemas: [ http://dublincore.org/2012/06/14/dcterms.rdf ]
+dct:contributor:
+  foaf:name: Andy Yang
+  foaf:mbox: mailto:ayang@oicr.on.ca
+dct:creator:
+  '@id': http://orcid.org/0000-0001-9102-5681
+  foaf:name: Andrey Kartashov
+  foaf:mbox: mailto:Andrey.Kartashov@cchmc.org
+dct:description: 'Developed at Cincinnati Children’s Hospital Medical Center for the
+  CWL consortium http://commonwl.org/ Original URL: https://github.com/common-workflow-language/workflows'
+cwlVersion: v1.0
+
+
+requirements:
+- class: DockerRequirement
+  dockerPull: quay.io/cancercollaboratory/dockstore-tool-samtools-sort:1.0
+inputs:
+  compression_level:
+    type: int?
+    inputBinding:
+      prefix: -l
+    doc: Set compression level, from 0 (uncompressed) to 9 (best)
+  input:
+    type: File
+    inputBinding:
+      position: 1
+
+    doc: Input bam file.
+  output_name:
+    type: string
+    inputBinding:
+      position: 2
+      prefix: -o
+
+    doc: Desired output filename.
+  sort_by_name:
+    type: boolean?
+    inputBinding:
+      prefix: -n
+
+    doc: Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.
+outputs:
+  output_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_name)
+
+arguments:
+ - prefix: -@
+   valueFrom: $(runtime.cores)
+ - prefix: -m
+   valueFrom: $(runtime.ram)M
+
+baseCommand: [samtools, sort]
+doc: |
+  Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary.
+
+  Usage: samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] -T out.prefix [-@ threads] [in.bam]
+
+  Options:
+  -l INT
+  Set the desired compression level for the final output file, ranging from 0 (uncompressed) or 1 (fastest but minimal compression) to 9 (best compression but slowest to write), similarly to gzip(1)'s compression level setting.
+
+  If -l is not used, the default compression level will apply.
+
+
+  -n
+  Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.
+
+  -o FILE
+  Write the final sorted output to FILE, rather than to standard output.
+
+  -O FORMAT
+  Write the final output as sam, bam, or cram.
+
+  By default, samtools tries to select a format based on the -o filename extension; if output is to standard output or no format can be deduced, -O must be used.
+
+  -T PREFIX
+  Write temporary files to PREFIX.nnnn.bam. This option is required.
+
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/star.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/star.cwl
index ddddabf..21d8b8e 100644
--- a/topmed-workflows/TOPMed_RNAseq_pipeline/star.cwl
+++ b/topmed-workflows/TOPMed_RNAseq_pipeline/star.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 doc: |
     A CWL wrapper for [run_STAR.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_STAR.py)
 
@@ -9,21 +10,42 @@ doc: |
 
 cwlVersion: v1.0
 class: CommandLineTool
-id: "run-star"
 label: "run-star"
-baseCommand: /src/run_STAR.py
+baseCommand: STAR
 
-requirements:
+hints:
   DockerRequirement:
-    dockerPull: heliumdatacommons/topmed-rnaseq:latest
+    #dockerPull: quay.io/biocontainers/star:2.5.3a--0
+    dockerFile: |
+      FROM debian:buster-slim
+      MAINTAINER biocontainers <biodocker@gmail.com>
+      LABEL    software="rna-star" \
+          container="rna-star" \
+          about.summary="ultrafast universal RNA-seq aligner" \
+          about.home="https://github.com/alexdobin/STAR/" \
+          software.version="2.5.3adfsg-1-deb" \
+          version="1" \
+          about.copyright="2009-2015 Alexander Dobin <dobin@cshl.edu>" \
+          about.license="GPL-3+" \
+          about.license_file="/usr/share/doc/rna-star/copyright" \
+          extra.binaries="/usr/bin/STAR" \
+          about.tags="biology::nucleic-acids, field::biology, field::biology:bioinformatics,:c++, role::program, use::analysing,:biological-sequence"
+      ENV DEBIAN_FRONTEND noninteractive
+      RUN echo \
+        'deb http://snapshot.debian.org/archive/debian/20170906/ buster  main' > /etc/apt/sources.list \
+        && printf "Package: r-*\nPin: origin snapshot.debian.org\nPin-Priority: 990\n" > /etc/apt/preferences.d/snapshot \
+        && apt-get -o Acquire::Check-Valid-Until=false update \
+        && apt-get upgrade -y \
+        && apt-get install -y --no-install-recommends \
+            --allow-unauthenticated rna-star=2.5.3a+dfsg-3 \
+        && apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/*
+    dockerImageId: star
 
 inputs:
   star_index:
     type: Directory
-    default:
-      type: Directory
     inputBinding:
-      position: 1
+      prefix: --genomeDir
   fastqs:
     type:
       type: array
@@ -31,26 +53,88 @@ inputs:
       inputBinding:
         itemSeparator: ","
     inputBinding:
-      position: 2
-  prefix_str:
+      prefix: --readFilesIn
+  prefix:
     type: string
     inputBinding:
-      position: 3
-  threads:
-    type: int?
-    inputBinding:
-      position: 5
-      prefix: --threads
+      prefix: --outFileNamePrefix
+      valueFrom: $(runtime.outdir)/$(self).
+
+arguments:
+  - prefix: --runMode
+    valueFrom: alignReads
+  - prefix: --runThreadN
+    valueFrom: $(runtime.cores)
+  - prefix: --twopassMode
+    valueFrom: Basic
+  - prefix: --outFilterMultimapNmax
+    valueFrom: "20"
+  - prefix: --alignSJoverhangMin
+    valueFrom: "8"
+  - prefix: --alignSJDBoverhangMin
+    valueFrom: "1"
+  - prefix: --outFilterMismatchNmax
+    valueFrom: "999"
+  - prefix: --outFilterMismatchNoverLmax
+    valueFrom: "0.1"
+  - prefix: --alignIntronMin
+    valueFrom: "20"
+  - prefix: --alignIntronMax
+    valueFrom: "1000000"
+  - prefix: --alignMatesGapMax
+    valueFrom: "1000000"
+  - prefix: --outFilterType
+    valueFrom: BySJout
+  - prefix: --outFilterScoreMinOverLread
+    valueFrom: "0.33"
+  - prefix: --outFilterMatchNminOverLread
+    valueFrom: "0.33"
+  - prefix: --limitSjdbInsertNsj
+    valueFrom: "1200000"
+  - prefix: --readFilesCommand
+    valueFrom: zcat
+  - prefix: --outSAMstrandField
+    valueFrom: introMotif
+  - prefix: --outFilterIntronMotifs
+    valueFrom: None
+  - prefix: --alignSoftClipAtReferenceEnds
+    valueFrom: Yes
+  - --quantMode
+  - TranscriptomeSAM
+  - GeneCounts
+  - --outSAMtype
+  - BAM
+  - Unsorted
+  - prefix: --outSAMunmapped
+    valueFrom: Within
+  - prefix: --genomeLoad
+    valueFrom: NoSharedMemory
+  - prefix: --chimSegmentMin
+    valueFrom: "15"
+  - prefix: --chimJunctionOverhangMin
+    valueFrom: "15"
+  - --chimOutType
+  - WithinBAM
+  - SoftClip
+  - prefix: --chimMainSegmentMultNmax
+    valueFrom: "1"
+  - --outSAMattributes
+  - NH
+  - HI
+  - AS
+  - nM
+  - NM
+  - ch
+  - --outSAMattrRGline
+  - ID:rg1
+  - SM:sm1
+
 
 outputs:
-  bam_file:
+  bam:
     type: File
     outputBinding:
-      glob: "*.Aligned.sortedByCoord.out.bam"
-  bam_index:
-    type: File
-    outputBinding:
-      glob: "*.Aligned.sortedByCoord.out.bam.bai"
+      glob: $(inputs.prefix).Aligned.out.bam
   transcriptome_bam:
     type: File
     outputBinding:
@@ -59,14 +143,18 @@ outputs:
     type: File
     outputBinding:
       glob: "*.Chimeric.out.junction"
-  chimeric_bam_file:
-    type: File
-    outputBinding:
-      glob: "*.Chimeric.out.sorted.bam"
-  chimeric_bam_index:
+  chimeric_bam:
     type: File
     outputBinding:
-      glob: "*.Chimeric.out.sorted.bam.bai"
+      glob: $(inputs.prefix).Chimeric.out.sam
+  # chimeric_bam_file:
+  #   type: File
+  #   outputBinding:
+  #     glob: "*.Chimeric.out.sorted.bam"
+  # chimeric_bam_index:
+  #   type: File
+  #   outputBinding:
+  #     glob: "*.Chimeric.out.sorted.bam.bai"
   read_counts:
     type: File
     outputBinding: