diff --git a/definitions/pipelines/bisulfite.cwl b/definitions/pipelines/bisulfite.cwl
index a6e3471ed..78392810e 100644
--- a/definitions/pipelines/bisulfite.cwl
+++ b/definitions/pipelines/bisulfite.cwl
@@ -7,27 +7,26 @@ requirements:
     - class: MultipleInputFeatureRequirement
     - class: SubworkflowFeatureRequirement
     - class: ScatterFeatureRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
 inputs:
     reference_index:
         type: string
     reference_sizes:
         type: File
-    instrument_data_bams:
-        type: File[]
-    read_group_id:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
+        doc: |
+          sequence represents the sequencing data as either FASTQs or BAMs with accompanying
+          readgroup information. Note that in the @RG field ID and SM are required.
     sample_name:
         type: string
-    trimming_adapters:
-        type: File
-    trimming_adapter_trim_end:
-        type: string
-    trimming_adapter_min_overlap:
-        type: int
-    trimming_max_uncalled:
-        type: int
-    trimming_min_readlength:
-        type: int
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
     QCannotation:
         type: File
     assay_non_cpg_sites:
@@ -54,31 +53,19 @@ outputs:
         type: Directory
         outputSource: bisulfite_qc/QC_directory
 steps:
-    bam_to_trimmed_fastq_and_biscuit_alignments:
-        run: ../subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl
-        scatter: [bam, read_group_id]
-        scatterMethod: dotproduct
+    bisulfite_alignment:
+        run: ../subworkflows/sequence_to_bisulfite_alignment.cwl
         in:
-            bam: instrument_data_bams
-            read_group_id: read_group_id
-            adapters: trimming_adapters
-            adapter_trim_end: trimming_adapter_trim_end
-            adapter_min_overlap: trimming_adapter_min_overlap
-            max_uncalled: trimming_max_uncalled
-            min_readlength: trimming_min_readlength
+            sequence: sequence
+            trimming_options: trimming_options
             reference_index: reference_index
+            sample_name: sample_name
         out:
             [aligned_bam]
-    merge:
-        run: ../tools/merge_bams.cwl
-        in:
-            bams: bam_to_trimmed_fastq_and_biscuit_alignments/aligned_bam
-        out:
-            [merged_bam]
     pileup:
         run: ../tools/biscuit_pileup.cwl
         in:
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
             reference: reference_index
         out:
             [vcf]
@@ -86,7 +73,7 @@ steps:
         run: ../subworkflows/bisulfite_qc.cwl
         in:
             vcf: pileup/vcf
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
             reference: reference_index
             QCannotation: QCannotation
         out:
@@ -110,7 +97,7 @@ steps:
         run: ../tools/bam_to_cram.cwl
         in:
             reference: reference_index
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
         out:
             [cram]
     index_cram:
diff --git a/definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl b/definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl
deleted file mode 100644
index fabf1e96f..000000000
--- a/definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-class: Workflow
-label: "bam to trimmed fastqs and biscuit alignments"
-requirements:
-    - class: SubworkflowFeatureRequirement
-inputs:
-    bam:
-        type: File
-    adapters:
-        type: File
-    adapter_trim_end:
-        type: string
-    adapter_min_overlap:
-        type: int
-    max_uncalled:
-        type: int
-    min_readlength:
-        type: int
-    read_group_id:
-        type: string
-    reference_index:
-        type: string
-outputs:
-    aligned_bam:
-        type: File
-        outputSource: biscuit_markdup/markdup_bam
-steps:
-    bam_to_fastq:
-        run: ../tools/bam_to_fastq.cwl
-        in:
-            bam: bam
-        out:
-            [fastq1, fastq2]
-    trim_fastq:
-        run: ../tools/trim_fastq.cwl
-        in:
-            reads1: bam_to_fastq/fastq1
-            reads2: bam_to_fastq/fastq2
-            adapters: adapters
-            adapter_trim_end: adapter_trim_end
-            adapter_min_overlap: adapter_min_overlap
-            max_uncalled: max_uncalled
-            min_readlength: min_readlength
-        out:
-            [fastq1, fastq2]
-    biscuit_align:
-        run: ../tools/biscuit_align.cwl
-        in:
-            reference_index: reference_index
-            fastq1: trim_fastq/fastq1
-            fastq2: trim_fastq/fastq2
-            read_group_id: read_group_id
-        out:
-            [aligned_bam]
-    index_bam:
-        run: ../tools/index_bam.cwl
-        in:
-            bam: biscuit_align/aligned_bam
-        out:
-            [indexed_bam]
-    biscuit_markdup:
-        run: ../tools/biscuit_markdup.cwl
-        in:
-           bam: index_bam/indexed_bam
-        out:
-            [markdup_bam]
diff --git a/definitions/subworkflows/sequence_to_bisulfite_alignment.cwl b/definitions/subworkflows/sequence_to_bisulfite_alignment.cwl
new file mode 100644
index 000000000..de3fd3e9e
--- /dev/null
+++ b/definitions/subworkflows/sequence_to_bisulfite_alignment.cwl
@@ -0,0 +1,64 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "take bisulfite sequence data through trimming, alignment, and markdup"
+requirements:
+    - class: SubworkflowFeatureRequirement
+    - class: ScatterFeatureRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
+inputs:
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
+        doc: "the unaligned sequence data with readgroup information"
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
+    reference_index:
+        type: string
+    sample_name:
+        type: string
+outputs:
+    aligned_bam:
+        type: File
+        outputSource: index_bam/indexed_bam
+steps:
+    trim_and_align:
+        scatter: [sequence]
+        scatterMethod: dotproduct
+        run: sequence_to_bisulfite_alignment_adapter.cwl
+        in:
+            sequence: sequence
+            trimming_options: trimming_options
+            reference_index: reference_index
+        out:
+            [aligned_bam]
+    merge:
+        run: ../tools/merge_bams_samtools.cwl
+        in:
+            bams: trim_and_align/aligned_bam
+            name: sample_name
+        out:
+            [merged_bam]
+    name_sort:
+        run: ../tools/name_sort.cwl
+        in:
+            bam: merge/merged_bam
+        out:
+            [name_sorted_bam]
+    biscuit_markdup:
+        run: ../tools/biscuit_markdup.cwl
+        in:
+           bam: name_sort/name_sorted_bam
+        out:
+            [markdup_bam]
+    index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: biscuit_markdup/markdup_bam
+        out:
+            [indexed_bam]
diff --git a/definitions/subworkflows/sequence_to_bisulfite_alignment_adapter.cwl b/definitions/subworkflows/sequence_to_bisulfite_alignment_adapter.cwl
new file mode 100644
index 000000000..687c15b1c
--- /dev/null
+++ b/definitions/subworkflows/sequence_to_bisulfite_alignment_adapter.cwl
@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "adapter for sequence_to_biscuit_alignments"
+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
+          - $import: ../types/trimming_options.yml
+    - class: StepInputExpressionRequirement
+    - class: SubworkflowFeatureRequirement
+inputs:
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data
+        doc: "the unaligned sequence data with readgroup information"
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
+    reference_index:
+        type: string
+outputs:
+    aligned_bam:
+        type: File
+        outputSource: biscuit_align/aligned_bam
+steps:
+     biscuit_align:
+        run: ../tools/biscuit_align.cwl
+        in:
+            bam:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)"
+            fastq1:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)"
+            fastq2:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)"
+            read_group:
+                source: sequence
+                valueFrom: $(self.readgroup)
+            trimming_options: trimming_options
+            reference_index: reference_index
+        out:
+            [aligned_bam]
diff --git a/definitions/tools/biscuit_align.cwl b/definitions/tools/biscuit_align.cwl
index 59f52f5fb..302134ea6 100644
--- a/definitions/tools/biscuit_align.cwl
+++ b/definitions/tools/biscuit_align.cwl
@@ -2,50 +2,130 @@
 
 cwlVersion: v1.0
 class: CommandLineTool
-label: "Biscuit: align"
-baseCommand: ["/bin/bash","biscuit_align.sh"]
+label: "Trim bisulfite reads and align usin biscuit"
+baseCommand: ["/bin/bash","biscuit_trim_and_align.sh"]
 requirements:
     - class: ResourceRequirement
       ramMin: 32000
       coresMin: 12
     - class: DockerRequirement
-      dockerPull: "mgibio/biscuit:0.3.8"
+      dockerPull: "mgibio/biscuit:0.3.16"
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
     - class: InitialWorkDirRequirement
       listing:
-      - entryname: 'biscuit_align.sh'
+      - entryname: 'biscuit_trim_and_align.sh'
         entry: |
-            set -eou pipefail
+            set -o pipefail
+            set -o errexit
+            set -o nounset
 
-            cores=$1
-            outdir="$2"
-            read_group_id="$3"
-            reference_index="$4"
-            fastq1="$5"
-            fastq2="$6"
+            RUN_TRIMMING="false"
 
-            /usr/bin/biscuit align -t $cores -M -R "$read_group_id" "$reference_index" "$fastq1" "$fastq2" | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t $cores -m 8G -o "$outdir/aligned.bam" /dev/stdin
+            while getopts "b:?1:?2:?g:r:n:d:t:?o:?" 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="$OPTARG"
+                        ;;
+                    d)
+                        OUTDIR="$OPTARG"
+                        ;;
+                    t)
+                        RUN_TRIMMING="true"
+                        TRIMMING_ADAPTERS="$OPTARG"
+                        ;;
+                    o)
+                        RUN_TRIMMING="true"
+                        TRIMMING_ADAPTER_MIN_OVERLAP="$OPTARG"
+                        ;;
+                esac
+            done
+
+            #reserve at least two cores for sorting
+            #if there are too few for this, let the scheduler sort it out
+            SORT_THREADS=2
+            if [[ $NTHREADS -gt 3 ]];then
+                NTHREADS=`expr $NTHREADS - $SORT_THREADS`
+            fi
+            #also reserve one core for trimming if it is specified
+            if [[ "$RUN_TRIMMING" == "true" ]];then
+                NTHREADS=`expr $NTHREADS - 1`
+            fi
+
+            if [[ "$MODE" == 'fastq' ]]; then
+                if [[ "$RUN_TRIMMING" == 'false' ]]; then
+                    /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin
+                else
+                    /opt/flexbar/flexbar --adapters "$TRIMMING_ADAPTERS" --reads "$FASTQ1" --reads2 "$FASTQ2" --adapter-trim-end LTAIL --adapter-min-overlap "$TRIMMING_ADAPTER_MIN_OVERLAP" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \
+                      | /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin
+                fi
+            fi
+            if [[ "$MODE" == 'bam' ]]; then
+                if [[ "$RUN_TRIMMING" == 'false' ]]; then
+                    /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin
+                else
+                    /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \
+                    | /opt/flexbar/flexbar --adapters "$TRIMMING_ADAPTERS" --adapter-trim-end LTAIL --adapter-min-overlap "$TRIMMING_ADAPTER_MIN_OVERLAP" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads -r - \
+                      | /usr/bin/biscuit align -t "$NTHREADS" -M -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t "$SORT_THREADS" -m 8G -o "$OUTDIR/aligned.bam" /dev/stdin
+                fi
+            fi
 
 arguments: [
-    { valueFrom: $(runtime.cores), position: -9 },
-    { valueFrom: $(runtime.outdir), position: -8 },
+    { valueFrom: $(runtime.cores), position: -9, prefix: '-n' },
+    { valueFrom: $(runtime.outdir), position: -8, prefix: '-d' },
 ]
 inputs:
     reference_index:
         type: string
         inputBinding:
             position: -3
+            prefix: '-r'
+    bam:
+        type: File?
+        inputBinding:
+            position: -5
+            prefix: '-b'
     fastq1:
-        type: File
+        type: File?
         inputBinding:
             position: -2
+            prefix: '-1'
     fastq2:
-        type: File
+        type: File?
         inputBinding:
             position: -1
-    read_group_id:
+            prefix: '-2'
+    read_group:
         type: string
         inputBinding:
             position: -4
+            prefix: '-g'
+    trimming_options:
+        type:
+          - ../types/trimming_options.yml#trimming_options
+          - "null"
+        inputBinding:
+            valueFrom: $( ['-t', self.adapters.path, '-o', self.min_overlap] )
 outputs:
     aligned_bam:
         type: File