diff --git a/definitions/pipelines/cle_aml_trio.cwl b/definitions/pipelines/cle_aml_trio.cwl
index dce91e30a..688c7fa68 100644
--- a/definitions/pipelines/cle_aml_trio.cwl
+++ b/definitions/pipelines/cle_aml_trio.cwl
@@ -7,28 +7,23 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_name:
         type: string?
         default: 'tumor'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_name:
         type: string?
         default: 'normal'
-    followup_bams:
-        type: File[]
-    followup_readgroups:
-        type: string[]
+    followup_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     followup_name:
         type: string?
         default: 'followup'
@@ -367,8 +362,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: normal_bams
-            readgroups: normal_readgroups
+            sequence: normal_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
@@ -391,8 +385,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: tumor_bams
-            readgroups: tumor_readgroups
+            sequence: tumor_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
@@ -415,8 +408,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: followup_bams
-            readgroups: followup_readgroups
+            sequence: followup_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/cle_somatic_exome.cwl b/definitions/pipelines/cle_somatic_exome.cwl
index 3337e329a..413ae0dc9 100644
--- a/definitions/pipelines/cle_somatic_exome.cwl
+++ b/definitions/pipelines/cle_somatic_exome.cwl
@@ -7,21 +7,18 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_name:
         type: string?
         default: 'tumor'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_name:
         type: string?
         default: 'normal'
@@ -295,8 +292,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: tumor_bams
-            readgroups: tumor_readgroups
+            sequence: tumor_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
@@ -319,8 +315,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: normal_bams
-            readgroups: normal_readgroups
+            sequence: normal_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/exome.cwl b/definitions/pipelines/exome.cwl
index 8048641b7..148b6c7fa 100644
--- a/definitions/pipelines/exome.cwl
+++ b/definitions/pipelines/exome.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -179,8 +178,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            sequence: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/exome_alignment.cwl b/definitions/pipelines/exome_alignment.cwl
index 976187eed..bd56f45be 100644
--- a/definitions/pipelines/exome_alignment.cwl
+++ b/definitions/pipelines/exome_alignment.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -92,11 +91,10 @@ outputs:
         outputSource: qc/verify_bam_id_depth
 steps:
     alignment:
-        run: ../subworkflows/bam_to_bqsr.cwl
+        run: ../subworkflows/sequence_to_bqsr.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            unaligned: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/gathered_cle_aml_trio.cwl b/definitions/pipelines/gathered_cle_aml_trio.cwl
index b02265c1b..761392e83 100644
--- a/definitions/pipelines/gathered_cle_aml_trio.cwl
+++ b/definitions/pipelines/gathered_cle_aml_trio.cwl
@@ -7,28 +7,23 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_name:
         type: string?
         default: 'tumor'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_name:
         type: string?
         default: 'normal'
-    followup_bams:
-        type: File[]
-    followup_readgroups:
-        type: string[]
+    followup_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     followup_name:
         type: string?
         default: 'followup'
@@ -189,14 +184,11 @@ steps:
         run: cle_aml_trio.cwl
         in:
             reference: reference
-            tumor_bams: tumor_bams
-            tumor_readgroups: tumor_readgroups
+            tumor_sequence: tumor_sequence
             tumor_name: tumor_name
-            normal_bams: normal_bams
-            normal_readgroups: normal_readgroups
+            normal_sequence: normal_sequence
             normal_name: normal_name
-            followup_bams: followup_bams
-            followup_readgroups: followup_readgroups
+            followup_sequence: followup_sequence
             followup_name: followup_name
             mills: mills
             known_indels: known_indels
diff --git a/definitions/pipelines/gathered_cle_somatic_exome.cwl b/definitions/pipelines/gathered_cle_somatic_exome.cwl
index 9a70899db..e8e713cb8 100644
--- a/definitions/pipelines/gathered_cle_somatic_exome.cwl
+++ b/definitions/pipelines/gathered_cle_somatic_exome.cwl
@@ -7,21 +7,18 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_cram_name:
         type: string?
         default: 'tumor.cram'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_cram_name:
         type: string?
         default: 'normal.cram'
@@ -152,11 +149,9 @@ steps:
         run: cle_somatic_exome.cwl
         in:
             reference: reference
-            tumor_bams: tumor_bams
-            tumor_readgroups: tumor_readgroups
+            tumor_sequence: tumor_sequence
             tumor_cram_name: tumor_cram_name
-            normal_bams: normal_bams
-            normal_readgroups: normal_readgroups
+            normal_sequence: normal_sequence
             normal_cram_name: normal_cram_name
             mills: mills
             known_indels: known_indels
diff --git a/definitions/pipelines/gathered_somatic_exome.cwl b/definitions/pipelines/gathered_somatic_exome.cwl
index 6d12c42ad..0d1e6f56d 100644
--- a/definitions/pipelines/gathered_somatic_exome.cwl
+++ b/definitions/pipelines/gathered_somatic_exome.cwl
@@ -7,21 +7,18 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_cram_name:
         type: string?
         default: 'tumor.cram'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_cram_name:
         type: string?
         default: 'normal.cram'
@@ -149,11 +146,9 @@ steps:
         run: somatic_exome.cwl
         in:
             reference: reference
-            tumor_bams: tumor_bams
-            tumor_readgroups: tumor_readgroups
+            tumor_sequence: tumor_sequence
             tumor_cram_name: tumor_cram_name
-            normal_bams: normal_bams
-            normal_readgroups: normal_readgroups
+            normal_sequence: normal_sequence
             normal_cram_name: normal_cram_name
             mills: mills
             known_indels: known_indels
diff --git a/definitions/pipelines/germline_exome.cwl b/definitions/pipelines/germline_exome.cwl
index 3103c8e95..0ad178adc 100644
--- a/definitions/pipelines/germline_exome.cwl
+++ b/definitions/pipelines/germline_exome.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -153,8 +152,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            sequence: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/germline_exome_hla_typing.cwl b/definitions/pipelines/germline_exome_hla_typing.cwl
index a610f5c16..b0e0be618 100644
--- a/definitions/pipelines/germline_exome_hla_typing.cwl
+++ b/definitions/pipelines/germline_exome_hla_typing.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -149,8 +148,7 @@ steps:
         run: germline_exome.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            sequence: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/germline_wgs.cwl b/definitions/pipelines/germline_wgs.cwl
index fb35e969e..5e6801be6 100644
--- a/definitions/pipelines/germline_wgs.cwl
+++ b/definitions/pipelines/germline_wgs.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -263,8 +262,7 @@ steps:
         run: wgs_alignment.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            sequence: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl
index 689bc42fa..ced9d2569 100644
--- a/definitions/pipelines/immuno.cwl
+++ b/definitions/pipelines/immuno.cwl
@@ -7,6 +7,7 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     #rnaseq inputs
@@ -53,17 +54,13 @@ inputs:
 
     #somatic inputs
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_name:
         type: string?
         default: 'tumor'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_name:
         type: string?
         default: 'normal'
@@ -641,11 +638,9 @@ steps:
         run: somatic_exome.cwl
         in:
             reference: reference
-            tumor_bams: tumor_bams
-            tumor_readgroups: tumor_readgroups
+            tumor_sequence: tumor_sequence
             tumor_name: tumor_name
-            normal_bams: normal_bams
-            normal_readgroups: normal_readgroups
+            normal_sequence: normal_sequence
             normal_name: normal_name
             mills: mills
             known_indels: known_indels
@@ -699,8 +694,7 @@ steps:
         run: germline_exome_hla_typing.cwl
         in:
             reference: reference
-            bams: normal_bams
-            readgroups: normal_readgroups
+            sequence: normal_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/somatic_exome.cwl b/definitions/pipelines/somatic_exome.cwl
index cf6380eb7..1c80978b2 100644
--- a/definitions/pipelines/somatic_exome.cwl
+++ b/definitions/pipelines/somatic_exome.cwl
@@ -7,21 +7,18 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
 inputs:
     reference: string
-    tumor_bams:
-        type: File[]
-    tumor_readgroups:
-        type: string[]
+    tumor_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     tumor_name:
         type: string?
         default: 'tumor'
-    normal_bams:
-        type: File[]
-    normal_readgroups:
-        type: string[]
+    normal_sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     normal_name:
         type: string?
         default: 'normal'
@@ -353,8 +350,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: tumor_bams
-            readgroups: tumor_readgroups
+            sequence: tumor_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
@@ -377,8 +373,7 @@ steps:
         run: exome_alignment.cwl
         in:
             reference: reference
-            bams: normal_bams
-            readgroups: normal_readgroups
+            sequence: normal_sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/wgs.cwl b/definitions/pipelines/wgs.cwl
index 348db2102..6f401bf0e 100644
--- a/definitions/pipelines/wgs.cwl
+++ b/definitions/pipelines/wgs.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -154,8 +153,7 @@ steps:
         run: wgs_alignment.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            sequence: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/pipelines/wgs_alignment.cwl b/definitions/pipelines/wgs_alignment.cwl
index fcb1ebfd5..60a8e6814 100644
--- a/definitions/pipelines/wgs_alignment.cwl
+++ b/definitions/pipelines/wgs_alignment.cwl
@@ -7,13 +7,12 @@ requirements:
     - class: SchemaDefRequirement
       types:
           - $import: ../types/labelled_file.yml
+          - $import: ../types/sequence_data.yml
     - class: SubworkflowFeatureRequirement
 inputs:
     reference: string
-    bams:
-        type: File[]
-    readgroups:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
     mills:
         type: File
         secondaryFiles: [.tbi]
@@ -99,11 +98,10 @@ outputs:
         outputSource: qc/bamcoverage_bigwig
 steps:
     alignment:
-        run: ../subworkflows/bam_to_bqsr.cwl
+        run: ../subworkflows/sequence_to_bqsr.cwl
         in:
             reference: reference
-            bams: bams
-            readgroups: readgroups
+            unaligned: sequence
             mills: mills
             known_indels: known_indels
             dbsnp_vcf: dbsnp_vcf
diff --git a/definitions/subworkflows/sequence_align_and_tag_adapter.cwl b/definitions/subworkflows/sequence_align_and_tag_adapter.cwl
new file mode 100644
index 000000000..f839ad013
--- /dev/null
+++ b/definitions/subworkflows/sequence_align_and_tag_adapter.cwl
@@ -0,0 +1,44 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "adapter for sequence_align_and_tag"
+doc: "Some workflow engines won't stage files in our nested structure, so parse it out here"
+requirements:
+    - class: InlineJavascriptRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+    - class: StepInputExpressionRequirement
+    - class: SubworkflowFeatureRequirement
+inputs:
+    unaligned:
+        type: ../types/sequence_data.yml#sequence_data
+        doc: "the unaligned sequence data with readgroup information"
+    reference:
+        type: string
+        doc: 'bwa-indexed reference file'
+outputs:
+    aligned_bam:
+        type: File
+        outputSource: align_and_tag/aligned_bam
+steps:
+    align_and_tag:
+        run: ../tools/sequence_align_and_tag.cwl
+        in:
+            reference: reference
+            bam:
+                source: unaligned
+                valueFrom: "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)"
+            fastq1:
+                source: unaligned
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)"
+            fastq2:
+                source: unaligned
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)"
+            readgroup:
+                source: unaligned
+                valueFrom: $(self.readgroup)
+
+        out:
+            [aligned_bam]
diff --git a/definitions/subworkflows/sequence_to_bqsr.cwl b/definitions/subworkflows/sequence_to_bqsr.cwl
new file mode 100644
index 000000000..aa9b81bbe
--- /dev/null
+++ b/definitions/subworkflows/sequence_to_bqsr.cwl
@@ -0,0 +1,93 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "Raw sequence data to BQSR"
+requirements:
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+    - class: ScatterFeatureRequirement
+    - class: SubworkflowFeatureRequirement
+    - class: MultipleInputFeatureRequirement
+
+inputs:
+    unaligned:
+        type: ../types/sequence_data.yml#sequence_data[]
+    bqsr_intervals:
+        type: string[]
+    reference:
+        type: string
+    dbsnp_vcf:
+        type: File
+        secondaryFiles: [.tbi]
+    final_name:
+        type: string?
+        default: 'final.bam'
+    mills:
+        type: File
+        secondaryFiles: [.tbi]
+    known_indels:
+        type: File
+        secondaryFiles: [.tbi]
+outputs:
+    final_bam:
+        type: File
+        outputSource: index_bam/indexed_bam
+        secondaryFiles: [.bai, ^.bai]
+    mark_duplicates_metrics_file:
+        type: File
+        outputSource: mark_duplicates_and_sort/metrics_file
+steps:
+    align:
+        scatter: [unaligned]
+        scatterMethod: dotproduct
+        run: sequence_align_and_tag_adapter.cwl
+        in:
+            unaligned: unaligned
+            reference: reference
+        out:
+            [aligned_bam]
+    merge:
+        run: ../tools/merge_bams_samtools.cwl
+        in:
+            bams: align/aligned_bam
+            name: final_name
+        out:
+            [merged_bam]
+    name_sort:
+        run: ../tools/name_sort.cwl
+        in:
+            bam: merge/merged_bam
+        out:
+            [name_sorted_bam]
+    mark_duplicates_and_sort:
+        run: ../tools/mark_duplicates_and_sort.cwl
+        in:
+            bam: name_sort/name_sorted_bam
+        out:
+            [sorted_bam, metrics_file]
+    bqsr:
+        run: ../tools/bqsr.cwl
+        in:
+            reference: reference
+            bam: mark_duplicates_and_sort/sorted_bam
+            intervals: bqsr_intervals
+            known_sites: [dbsnp_vcf, mills, known_indels]
+        out:
+            [bqsr_table]
+    apply_bqsr:
+        run: ../tools/apply_bqsr.cwl
+        in:
+            reference: reference
+            bam: mark_duplicates_and_sort/sorted_bam
+            bqsr_table: bqsr/bqsr_table
+            output_name: final_name
+        out:
+            [bqsr_bam]
+    index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: apply_bqsr/bqsr_bam
+        out:
+            [indexed_bam]
diff --git a/definitions/tools/sequence_align_and_tag.cwl b/definitions/tools/sequence_align_and_tag.cwl
new file mode 100644
index 000000000..0f9deadc7
--- /dev/null
+++ b/definitions/tools/sequence_align_and_tag.cwl
@@ -0,0 +1,87 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+label: "align with bwa_mem and tag"
+doc: "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this"
+baseCommand: ["/bin/bash", "sequence_alignment_helper.sh"]
+requirements:
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+    - class: ResourceRequirement
+      coresMin: 8
+      ramMin: 20000
+    - class: DockerRequirement
+      dockerPull: "mgibio/alignment_helper-cwl:1.0.0"
+    - class: InitialWorkDirRequirement
+      listing:
+      - entryname: 'sequence_alignment_helper.sh'
+        entry: |
+            set -o pipefail
+            set -o errexit
+            set -o nounset
+
+            while getopts "b:?1:?2:?g:r:n:" opt; do
+                case "$opt" in
+                    b)
+                        MODE=bam
+                        BAM="$OPTARG"
+                        ;;
+                    1)
+                        MODE=fastq
+                        FASTQ1="$OPTARG"
+                        ;;
+                    2)  
+                        MODE=fastq
+                        FASTQ2="$OPTARG"
+                        ;;
+                    g)
+                        READGROUP="$OPTARG"
+                        ;;
+                    r)
+                        REFERENCE="$OPTARG"
+                        ;;
+                    n)
+                        NTHREADS="$OPTARG"
+                        ;;
+                esac
+            done
+
+            if [[ "$MODE" == 'fastq' ]]; then
+                /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin
+            fi
+            if [[ "$MODE" == 'bam' ]]; then
+                /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin
+            fi
+stdout: "refAlign.bam"
+arguments:
+    - valueFrom: $(runtime.cores)
+      position: 5
+      prefix: '-n'
+inputs:
+    bam:
+        type: File?
+        inputBinding:
+            prefix: '-b'
+    fastq1:
+        type: File?
+        inputBinding:
+            prefix: '-1'
+    fastq2:
+        type: File?
+        inputBinding:
+            prefix: '-2'
+    readgroup:
+        type: string
+        inputBinding:
+            prefix: '-g'
+    reference:
+        type: string
+        inputBinding:
+            position: 4
+            prefix: '-r'
+        doc: 'bwa-indexed reference file'
+outputs:
+    aligned_bam:
+        type: stdout
diff --git a/definitions/types/sequence_data.yml b/definitions/types/sequence_data.yml
new file mode 100644
index 000000000..324e059a2
--- /dev/null
+++ b/definitions/types/sequence_data.yml
@@ -0,0 +1,20 @@
+type: record
+name: sequence_data
+label: sequence data with readgroup information
+fields:
+    sequence:
+        type:
+            - type: record
+              name: bam
+              fields:
+                  bam:
+                      type: File
+            - type: record
+              name: fastqs
+              fields:
+                  fastq1:
+                      type: File
+                  fastq2:
+                      type: File
+    readgroup:
+        type: string
diff --git a/example_data/cle_IDT_somatic_exome_template.yaml b/example_data/cle_IDT_somatic_exome_template.yaml
index f44a6f2c4..0b7cb3851 100644
--- a/example_data/cle_IDT_somatic_exome_template.yaml
+++ b/example_data/cle_IDT_somatic_exome_template.yaml
@@ -54,11 +54,12 @@ varscan_strand_filter: 1
 varscan_min_var_freq: 0.08
 varscan_p_value: 0.1
 varscan_max_normal_freq: 0.1
-normal_bams:
-- class: File
-  path: NORMAL_BAM_PATH
-normal_readgroups:
-- "NORMAL_RG_STR"
+normal_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: NORMAL_BAM_PATH
+    readgroup: "NORMAL_RG_STR"
 omni_vcf:
   class: File
   path: /gscmnt/gc2709/info/production_reference_GRCh38DH/accessory_vcf/omni25-ld-pruned-20000-2000-0.5-annotated.wchr.sites_only.b38.autosomes_only.vcf.gz
@@ -76,11 +77,12 @@ synonyms_file:
 target_intervals:
   class: File
   path: /gscmnt/gc2709/info/production_reference_GRCh38DH/CLE/IDTExome/xgen-exome-research-panel-targets.interval_list
-tumor_bams:
-- class: File
-  path: TUMOR_BAM_PATH 
-tumor_readgroups:
-- "TUMOR_RG_STR"
+tumor_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: TUMOR_BAM_PATH
+    readgroup: "TUMOR_RG_STR"
 filter_docm_variants: true
 filter_minimum_depth: 20
 cle_vcf_filter: true
diff --git a/example_data/cle_aml_trio_template.yaml b/example_data/cle_aml_trio_template.yaml
index 232d0f46b..898655c59 100644
--- a/example_data/cle_aml_trio_template.yaml
+++ b/example_data/cle_aml_trio_template.yaml
@@ -87,11 +87,12 @@ varscan_strand_filter: 1
 varscan_min_var_freq: 0.08
 varscan_p_value: 0.1
 varscan_max_normal_freq: 0.1
-normal_bams:
-- class: File
-  path: NORMAL_BAM_PATH
-normal_readgroups:
-- "NORMAL_RG_STR"
+normal_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: NORMAL_BAM_PATH
+    readgroup: "NORMAL_RG_STR"
 omni_vcf:
   class: File
   path: /gscmnt/gc2709/info/production_reference_GRCh38DH/accessory_vcf/omni25-ld-pruned-20000-2000-0.5-annotated.wchr.sites_only.b38.autosomes_only.vcf.gz
@@ -116,16 +117,18 @@ synonyms_file:
 target_intervals:
   class: File
   path: /gscmnt/gc13016/cle/54f8f7b915cb472aa183c721307369ab_scratch_space/new_AML_trio/new_cwl/bed_file/IDT_targets_plus50bp_build38.resorted.merged.interval_list
-tumor_bams:
-- class: File
-  path: TUMOR_BAM_PATH 
-tumor_readgroups:
-- "TUMOR_RG_STR"
-followup_bams:
-- class: File
-  path: FOLLOWUP_BAM_PATH 
-followup_readgroups:
-- "FOLLOWUP_RG_STR"
+tumor_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: TUMOR_BAM_PATH
+    readgroup: "TUMOR_RG_STR"
+followup_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: FOLLOWUP_BAM_PATH
+    readgroup: "FOLLOWUP_RG_STR"
 filter_docm_variants: false
 filter_minimum_depth: 20
 annotate_coding_only: false
diff --git a/example_data/exome_workflow.yaml b/example_data/exome_workflow.yaml
index d96ff75e5..ae3ae7175 100644
--- a/example_data/exome_workflow.yaml
+++ b/example_data/exome_workflow.yaml
@@ -2,11 +2,6 @@
 bait_intervals:
   class: File
   path: exome_workflow/chr17_test_bait.interval_list
-bams:
-- class: File
-  path: exome_workflow/2895499223.bam
-- class: File
-  path: exome_workflow/2895499237.bam
 bqsr_intervals:
 - chr17
 custom_gnomad_vcf:
@@ -40,11 +35,19 @@ per_target_intervals:
   class: File
   path: exome_workflow/chr17_test_target.interval_list
 picard_metric_accumulation_level: ALL_READS
-readgroups:
-- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
-- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
 reference: /gscmnt/gc2764/cad/jwalker/toil_test/cancer-genomics-workflow/example_data/exome_workflow/chr17_test.fa
 sample_name: H_NJ-HCC1395-HCC1395
+sequence:
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499223.bam
+    readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499237.bam
+    readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
 synonyms_file:
   class: File
   path: exome_workflow/chromAlias.ensembl.txt
diff --git a/example_data/germline_exome.yaml b/example_data/germline_exome.yaml
index f1ccc9ab8..c789dbff1 100644
--- a/example_data/germline_exome.yaml
+++ b/example_data/germline_exome.yaml
@@ -2,11 +2,6 @@
 bait_intervals:
   class: File
   path: exome_workflow/chr17_test_bait.interval_list
-bams:
-- class: File
-  path: exome_workflow/2895499223.bam
-- class: File
-  path: exome_workflow/2895499237.bam
 bqsr_intervals:
 - chr17
 custom_gnomad_vcf:
@@ -47,10 +42,18 @@ summary_intervals:
       class: File
       path: exome_workflow/chr17_test_genes.interval_list
 picard_metric_accumulation_level: ALL_READS
-readgroups:
-- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
-- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
 reference: "/gscmnt/gc2764/cad/jgarza/shared/exome_workflow/chr17_test.fa"
+sequence:
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499223.bam
+    readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499237.bam
+    readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
 synonyms_file:
   class: File
   path: exome_workflow/chromAlias.ensembl.txt
diff --git a/example_data/germline_wgs.yaml b/example_data/germline_wgs.yaml
index 4ae5b7e6d..42b2b4433 100644
--- a/example_data/germline_wgs.yaml
+++ b/example_data/germline_wgs.yaml
@@ -1,9 +1,4 @@
 ---
-bams:
-- class: File
-  path: exome_workflow/2895499223.bam
-- class: File
-  path: exome_workflow/2895499237.bam
 bqsr_intervals: ["chr17"]
 custom_gnomad_vcf:
   class: File
@@ -32,9 +27,17 @@ qc_intervals:
     class: File
     path: exome_workflow/chr17_test_bait.interval_list
 reference: "/gscmnt/gc2764/cad/jgarza/pipeline_data/exome_workflow/chr17_test.fa"
-readgroups:
-- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
-- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+sequence:
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499223.bam
+    readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499237.bam
+    readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
 summary_intervals:
     [ {label: "genes", file: { class: File, path: 'exome_workflow/chr17_test_genes.interval_list' }} ]
 synonyms_file:
diff --git a/example_data/somatic_exome.yaml b/example_data/somatic_exome.yaml
index 49619cfb8..856d12bf2 100644
--- a/example_data/somatic_exome.yaml
+++ b/example_data/somatic_exome.yaml
@@ -2,22 +2,28 @@
 bait_intervals:
   class: File
   path: exome_workflow/chr17_test_bait.interval_list
-tumor_bams:
-- class: File
-  path: exome_workflow/2895499223.bam
-- class: File
-  path: exome_workflow/2895499237.bam
-tumor_readgroups:
-- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
-- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
-normal_bams:
-- class: File
-  path: exome_workflow/2895499331.bam
-- class: File
-  path: exome_workflow/2895499399.bam
-normal_readgroups:
-- "@RG\tID:2895499331\tPU:H7HY2CCXX.3.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC"
-- "@RG\tID:2895499399\tPU:H7HY2CCXX.4.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC"
+tumor_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499223.bam
+    readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499237.bam
+    readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC"
+normal_sequence:
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499331.bam
+    readgroup: "@RG\tID:2895499331\tPU:H7HY2CCXX.3.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC"
+  - sequence:
+      bam:
+        class: File
+        path: exome_workflow/2895499399.bam
+    readgroup: "@RG\tID:2895499399\tPU:H7HY2CCXX.4.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC"
 custom_gnomad_vcf:
   class: File
   path: exome_workflow/chr17_test_gnomADe.vcf.gz