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+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
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+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..b722356
--- /dev/null
+++ b/README.md
@@ -0,0 +1,36 @@
+[`pggb`](https://github.com/pangenome/pggb/) builds pangenome variation graphs from a set of input sequences. `pggb.cwl` is a port of `pggb` to the [Common Workflow Language](https://www.commonwl.org/) (CWL).
+
+# Features
+
+`pggb.cwl` offers:
+- better parallelization, especially of the wfmash all-to-all alignment step and the various visualization steps
+- more readable code
+- reproducible
+- portable across computing environments
+
+# How to use
+
+First, compile the [ccwl](https://ccwl.systemreboot.net/) sources to a CWL workflow.
+```
+ccwl compile -o pggb.cwl pggb.scm
+```
+Now, run the compiled CWL workflow using your preferred CWL implementation. For cwltool, the reference CWL implementation:
+```
+cwltool pggb.cwl inputs.yaml
+```
+[ravanan](https://forge.systemreboot.net/ravanan/) is a CWL implementation that uses [Guix](https://guix.gnu.org/) to provide robust reproducibility guarantees. To run `pggb.cwl` using ravanan:
+```
+ravanan --guix-channels=channels.scm --store=store pggb.cwl inputs.yaml
+```
+You may need to pass in more options based on the specifics of your computing environment.
+
+# Differences
+
+`pggb.cwl` deviates from `pggb` in the following:
+- Number of haplotypes is always required. In contrast, this is optional in `pggb` if sequences follow the [PanSN-spec](https://github.com/pangenome/PanSN-spec).
+- External mappers are not supported.
+- `--vcf-spec` is not implemented.
+
+# License
+
+pggb.cwl is free software released under the terms of the [GNU General Public License](https://www.gnu.org/licenses/gpl.html), either version 3 of the License, or (at your option) any later version.
diff --git a/channels.scm b/channels.scm
new file mode 100644
index 0000000..bc0b6a3
--- /dev/null
+++ b/channels.scm
@@ -0,0 +1,25 @@
+(list (channel
+        (name 'gn-bioinformatics)
+        (url "https://git.genenetwork.org/guix-bioinformatics")
+        (commit "e292b4024739e2f3bc2a2f9335b430dceb75a654"))
+      (channel
+        (inherit %default-guix-channel)
+        (commit "99556e7724b3dd65e2be0dd06b7b69695c9c7901"))
+      (channel
+        (name 'guix-past)
+        (url "https://codeberg.org/guix-science/guix-past")
+        (commit "d0e01528abcf07a40981303b3e4a54edd7ffd501")
+        (introduction
+         (make-channel-introduction
+          "0c119db2ea86a389769f4d2b9c6f5c41c027e336"
+          (openpgp-fingerprint
+           "3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"))))
+      (channel
+        (name 'guix-rust-past-crates)
+        (url "https://codeberg.org/guix/guix-rust-past-crates")
+        (commit "20997ccc759799c19709fdde729d67e470fa5bcf")
+        (introduction
+         (make-channel-introduction
+          "1db24ca92c28255b28076792b93d533eabb3dc6a"
+          (openpgp-fingerprint
+           "F4C2D1DF3FDEEA63D1D30776ACC66D09CA528292")))))
diff --git a/manifest.scm b/manifest.scm
new file mode 100644
index 0000000..25c9de1
--- /dev/null
+++ b/manifest.scm
@@ -0,0 +1,41 @@
+(use-modules ((gnu packages bioinformatics) #:select (ccwl ravanan) #:prefix guix:)
+             ((gnu packages graphviz) #:select (graphviz))
+             ((gnu packages web) #:select (jq))
+             (guix git-download)
+             (guix packages))
+
+(define ccwl
+  (let ((commit "a83645270da5c0ee3f494b6f0449b0611fde968a")
+        (revision "0"))
+    (package
+      (inherit guix:ccwl)
+      (name "ccwl")
+      (version (git-version "0.5.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://git.systemreboot.net/ccwl")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0gr367hiki854dkrwbhcr55f3q8aiqvk25cldx3raqy0prd3xagw")))))))
+
+(define ravanan
+  (let ((commit "41db9dc5ab7e14c8c0fb7d669a615c62c4008916"))
+    (package
+      (inherit guix:ravanan)
+      (name "ravanan")
+      (version "0.2.0")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://git.systemreboot.net/ravanan")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0xb0568g6l4rf5zibrai5zra9afwgnjxiflik6mdqkv2hi32c7rl")))))))
+
+(packages->manifest
+ (list ccwl ravanan jq graphviz))
diff --git a/pggb.scm b/pggb.scm
new file mode 100644
index 0000000..595cb97
--- /dev/null
+++ b/pggb.scm
@@ -0,0 +1,506 @@
+;;; pggb.cwl --- CWL port of pggb
+;;; Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net>
+;;;
+;;; This file is part of pggb.cwl.
+;;;
+;;; pggb.cwl is free software: you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation, either version 3 of the License, or
+;;; (at your option) any later version.
+;;;
+;;; pggb.cwl is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+;;; General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with pggb.cwl.  If not, see <https://www.gnu.org/licenses/>.
+
+;;;
+;;; This is a port of pggb 0.7.4 to CWL.
+;;;
+
+(define gzip
+  (command #:inputs (file #:type File)
+           #:run "gzip" "--to-stdout" file
+           #:stdout "$(inputs.file.basename).gz"
+           #:outputs (compressed-file #:type File
+                                      #:binding ((glob . "$(inputs.file.basename).gz")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "gzip")))))))))
+
+(define bgzip
+  (command #:inputs (fasta #:type File) (threads #:type int)
+           #:run "bgzip" ("-@" threads) "--stdout" fasta
+           #:outputs (compressed-fasta #:type stdout
+                                       #:other ((secondaryFiles . #(".gzi"))))
+           #:stdout "$(inputs.fasta.basename).gz"
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "htslib")))))))))
+
+(define samtools-faidx
+  (command #:inputs (compressed_fasta #:type File
+                                      #:stage? #t)
+           #:run "samtools" "faidx" "$(inputs.compressed_fasta.basename)"
+           #:outputs (indexed-fasta #:type File
+                                    #:binding ((glob . "$(inputs.compressed_fasta.basename)"))
+                                    #:other ((secondaryFiles . #(".fai" ".gzi"))))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "samtools")))))))))
+
+(define wfmash-approximate
+  (command #:inputs
+           (sequences #:type File
+                      #:other ((secondaryFiles . #(".fai" ".gzi"))))
+           (number_of_haplotypes #:type int)
+           (segment_length #:type int)
+           (block_length #:type #(int null))
+           (map-percent-identity #:type int)
+           (num-mappings-for-segment #:type int)
+           (no-split #:type boolean)
+           (sparsify_mappings #:type #(float null))
+           (kmer-size #:type int)
+           (kmer-threshold #:type float)
+           (exclude-delimiter #:type string)
+           (hg-filter-ani-diff #:type float)
+           (no-merge #:type boolean)
+           (threads #:type int)
+           #:run
+           "wfmash"
+           ("--segment-length" segment_length)
+           ("--block-length" "$(inputs.block_length === null ? 5*inputs.segment_length : inputs.block_length)")
+           ("--map-pct-id" map-percent-identity)
+           ("--num-mappings-for-segment" num-mappings-for-segment)
+           ("--no-split" no-split)
+           ;; Set sparse mapping using giant component heuristic: we
+           ;; keep 10*log(n)/n mappings if this is less than 1,
+           ;; otherwise we keep all.
+           ("--sparsify-mappings" "$(inputs.sparsify_mappings === null ? Math.min(10*Math.log(inputs.number_of_haplotypes)/inputs.number_of_haplotypes, 1) : inputs.sparsify_mappings)")
+           ("--kmer" kmer-size)
+           ("--kmer-threshold" kmer-threshold)
+           "--skip-self"
+           ("--skip-prefix" exclude-delimiter)
+           ("--threads" threads)
+           "--lower-triangular"
+           ("--hg-filter-ani-diff" hg-filter-ani-diff)
+           "--approx-map"
+           ("--no-merge" no-merge)
+           sequences
+           #:outputs (approximate-pairwise-alignment #:type stdout)
+           #:stdout "$(inputs.sequences.nameroot).paf"
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "wfmash")))))))))
+
+(define split-pairwise-alignment
+  (command #:inputs (pairwise_alignment #:stage? #t) (chunks #:type int)
+           #:run "split_approx_mappings_in_chunks" pairwise_alignment chunks
+           #:outputs (pairwise-alignment-chunks #:type (array File)
+                                                #:binding ((glob . "$(inputs.pairwise_alignment.basename).chunk_*.paf")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "wfmash")))))))))
+
+(define wfmash
+  (command #:inputs
+           (sequences #:type File
+                      #:other ((secondaryFiles . #(".fai" ".gzi"))))
+           (number_of_haplotypes #:type int)
+           (segment_length #:type int)
+           (block_length #:type #(int null))
+           (map-percent-identity #:type int)
+           (num-mappings-for-segment #:type int)
+           (no-split #:type boolean)
+           (sparsify_mappings #:type #(float null))
+           (kmer-size #:type int)
+           (kmer-threshold #:type float)
+           (exclude-delimiter #:type string)
+           (hg-filter-ani-diff #:type float)
+           (no-merge #:type boolean)
+           (input-paf #:type File)
+           (threads #:type int)
+           #:run
+           "wfmash"
+           ("--segment-length" segment_length)
+           ("--block-length" "$(inputs.block_length === null ? 5*inputs.segment_length : inputs.block_length)")
+           ("--map-pct-id" map-percent-identity)
+           ("--num-mappings-for-segment" num-mappings-for-segment)
+           ("--no-split" no-split)
+           ;; Set sparse mapping using giant component heuristic: we
+           ;; keep 10*log(n)/n mappings if this is less than 1,
+           ;; otherwise we keep all.
+           ("--sparsify-mappings" "$(inputs.sparsify_mappings === null ? Math.min(10*Math.log(inputs.number_of_haplotypes)/inputs.number_of_haplotypes, 1) : inputs.sparsify_mappings)")
+           ("--kmer" kmer-size)
+           ("--kmer-threshold" kmer-threshold)
+           "--skip-self"
+           ("--skip-prefix" exclude-delimiter)
+           ("--threads" threads)
+           "--lower-triangular"
+           ("--hg-filter-ani-diff" hg-filter-ani-diff)
+           ("--no-merge" no-merge)
+           ("--input-paf" input-paf)
+           sequences
+           #:outputs (pairwise-alignment #:type stdout)
+           #:stdout "$(inputs.sequences.nameroot).paf"
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "wfmash")))))))))
+
+(define seqwish
+  (command #:inputs
+           (sequences #:type File)
+           (pairwise-alignments #:type (array File))
+           (min-match-length #:type int)
+           (sparse-factor #:type float)
+           (transclose-batch #:type string)
+           (threads #:type int)
+           #:run
+           "seqwish"
+           ("--seqs" sequences)
+           ("--paf-alns" (array pairwise-alignments #:separator ","))
+           ("--min-match-len" min-match-length)
+           ("--sparse-factor" sparse-factor)
+           ("--transclose-batch" transclose-batch)
+           ("--threads" threads)
+           ("-g" "$(inputs.sequences.nameroot).gfa")
+           #:outputs (variation-graph #:type File
+                                      #:binding ((glob . "$(inputs.sequences.nameroot).gfa")))
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "seqwish")))))))))
+
+(define smoothxg
+  (command #:inputs
+           (graph #:type File)
+           (number_of_haplotypes #:type int)
+           (consensus-prefix #:type string)
+           (map_percent_identity #:type int)
+           (maximum-path-jump #:type string)
+           (maximum-edge-jump #:type string)
+           (abpoa #:type boolean)
+           (global-poa #:type boolean)
+           (poa-target-lengths #:type (array string))
+           (poa_params #:type string)
+           (poa-padding-ratio #:type float)
+           (poa_maximum_pad_depth #:type int)
+           (threads #:type int)
+           #:run
+           "smoothxg"
+           ("--gfa-in" graph)
+           ("--n-haps" number_of_haplotypes)
+           ("--chop-to" "100")
+           ("--block-id-min" "$(inputs.map_percent_identity / 100)")
+           ("--block-ratio-min" "0")
+           ("--path-jump-max" maximum-path-jump)
+           ("--edge-jump-max" maximum-edge-jump)
+           ("--poa-length-targets" (array poa-target-lengths
+                                          #:separator ","))
+           ("--poa-params" "${switch (inputs.poa_params) { case \"asm5\": return \"1,19,39,3,81,1\"; case \"asm10\": return \"1,9,16,2,41,1\"; case \"asm15\": return \"1,7,11,2,33,1\"; case \"asm20\": return \"1,4,6,2,26,1\"; default: return inputs.poa_params }}")
+           ("--poa-padding-ratio" poa-padding-ratio)
+           ("--max-block-depth-adaptive-poa-padding" "$(inputs.poa_maximum_pad_depth * inputs.number_of_haplotypes)")
+           ("--min-block-depth-split" "0")
+           ("--min-block-depth-mash" "0")
+           ("--abpoa" abpoa)
+           ("--change-alignment-mode" global-poa)
+           ("--write-msa-in-maf-format" "$(inputs.graph.nameroot).maf")
+           ("--consensus-prefix" consensus-prefix)
+           ;; Consensus paths are temporarily disabled in pggb.
+           "--vanish-consensus"
+           ("--threads" threads)
+           ("--smoothed-out" "$(inputs.graph.nameroot).gfa")
+           #:outputs
+           (smoothed-graph #:type File
+                           #:binding ((glob . "$(inputs.graph.nameroot).gfa")))
+           (multiple-sequence-alignment #:type File
+                                        #:binding ((glob . "$(inputs.graph.nameroot).maf")))
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "smoothxg")))))))))
+
+(define gfaffix
+  (command #:inputs (graph #:type File)
+           #:run "gfaffix" graph ("--output_refined" "$(inputs.graph.nameroot).fix.gfa")
+           #:stdout "$(inputs.graph.nameroot).fix.affixes.tsv"
+           #:outputs
+           (fixed-graph #:type File
+                        #:binding ((glob . "$(inputs.graph.nameroot).fix.gfa")))
+           (fix-affixes #:type stdout)
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "gfaffix")))))))))
+
+(define odgi-build
+  (command #:inputs graph (threads #:type int)
+           ;; Unlike pggb, we preserve the graph segment IDs; we do
+           ;; not optimize them away using --optimize.
+           #:run "odgi" "build" ("-t" threads) ("--gfa" graph) ("--out" "$(inputs.graph.nameroot).og")
+           #:outputs (odgi-graph #:binding ((glob . "$(inputs.graph.nameroot).og")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-view
+  (command #:inputs graph
+           #:run "odgi" "view" "--to-gfa" ("--idx" graph)
+           #:stdout "$(inputs.graph.nameroot).gfa"
+           #:outputs (gfa-graph #:type stdout)
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+
+(define odgi-unchop
+  (command #:inputs graph (threads #:type int)
+           #:run "odgi" "unchop" ("-t" threads) ("--idx" graph) ("--out" "$(inputs.graph.nameroot).og")
+           #:outputs (unchopped-graph #:binding ((glob . "$(inputs.graph.nameroot).og")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-sort
+  (command #:inputs graph (threads #:type int)
+           #:run "odgi" "sort" ("--pipeline" "Ygs") ("-t" threads) ("--idx" graph) ("--out" "$(inputs.graph.nameroot).og")
+           #:outputs (sorted-graph #:binding ((glob . "$(inputs.graph.nameroot).og")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-stats
+  (command #:inputs graph
+           #:run "odgi" "stats" ("--idx" graph) "--multiqc" "--sum-path-nodes-distances" "--no-gap-links" "--penalize-different-orientation" "--mean-links-length"
+           #:stdout "$(inputs.graph.nameroot).stats.yaml"
+           #:outputs (stats #:type stdout)
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-viz
+  (command #:inputs graph (width #:type int #:default 1500) (height #:type int #:default 500) (path-height #:type int #:default 10) (ignore-prefix #:type string) (white-to-black #:type boolean #:default #f) (change-darkness #:type boolean #:default #f) (color-by-mean-depth #:type boolean #:default #f) (color-by-mean-inversion-rate #:type boolean #:default #f) (compressed-mode #:type boolean #:default #f) (color-by-uncalled-bases #:type boolean #:default #f)
+           #:run "odgi" "viz" ("--width" width) ("--height" height) ("--ignore-prefix" ignore-prefix) ("--white-to-black" white-to-black) ("--change-darkness" change-darkness) ("--color-by-mean-depth" color-by-mean-depth) ("--color-by-mean-inversion-rate" color-by-mean-inversion-rate) ("--compressed-mode" compressed-mode) ("--color-by-uncalled-bases" color-by-uncalled-bases) ("--idx" graph) ("--out" "$(inputs.graph.nameroot).png")
+           #:outputs (visualization #:binding ((glob . "$(inputs.graph.nameroot).png")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-layout
+  (command #:inputs graph (threads #:type int)
+           #:run "odgi" "layout" ("--threads" threads) ("--idx" graph) ("--out" "$(inputs.graph.nameroot).lay")
+           #:outputs (layout #:binding ((glob . "$(inputs.graph.nameroot).lay")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define odgi-draw
+  (command #:inputs graph layout (height #:type int #:default 1000) (color-paths #:type boolean #:default #f) (line-width #:type int #:default 10)
+           #:run "odgi" "draw" ("--idx" graph) ("--coords-in" layout) ("--png" "$(inputs.graph.nameroot).png") ("--png-height" height) ("--color-paths" color-paths) ("--line-width" line-width)
+           #:outputs (visualization-2d #:binding ((glob . "$(inputs.graph.nameroot).png")))
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "odgi")))))))))
+
+(define reduce-redundancy
+  (workflow (graph (threads #:type int))
+    (pipe (gfaffix #:graph graph)
+          (odgi-build #:graph fixed-graph
+                      #:threads threads)
+          (odgi-unchop #:graph odgi-graph
+                       #:threads threads)
+          (odgi-sort #:graph unchopped-graph
+                     #:threads threads)
+          (rename #:reduced-graph sorted-graph))))
+
+(define visualize
+  (workflow (graph (ignore-prefix #:type string))
+    (tee (pipe (odgi-viz (default-visualize)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix)
+               (rename #:default-visualization visualization))
+         (pipe (odgi-viz (visualize-by-nucleotide-position)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix
+                         #:white-to-black #t
+                         #:change-darkness #t)
+               (rename #:visualization-by-nucleotide-position visualization))
+         (pipe (odgi-viz (visualize-by-mean-depth)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix
+                         #:color-by-mean-depth #t)
+               (rename #:visualization-by-mean-depth visualization))
+         (pipe (odgi-viz (visualize-by-mean-inversion-rate)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix
+                         #:color-by-mean-inversion-rate #t)
+               (rename #:visualization-by-mean-inversion-rate visualization))
+         (pipe (odgi-viz (visualize-with-compressed-mode)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix
+                         #:compressed-mode #t)
+               (rename #:compressed-mode-visualization visualization))
+         (pipe (odgi-viz (visualize-by-uncalled-bases)
+                         #:graph graph
+                         #:ignore-prefix ignore-prefix
+                         #:color-by-uncalled-bases #t)
+               (rename #:visualization-by-uncalled-bases visualization)))))
+
+(define visualize-2d
+  (workflow (graph (threads #:type int))
+    (pipe (odgi-layout #:graph graph
+                       #:threads threads)
+          (tee (pipe (odgi-draw (default-visualize-2d)
+                                #:graph graph
+                                #:layout layout)
+                     (rename #:default-visualization-2d visualization-2d))
+               (pipe (odgi-draw (visualize-2d-with-paths)
+                                #:graph graph
+                                #:layout layout
+                                #:color-paths #t
+                                #:line-width 20)
+                     (rename #:visualization-2d-with-paths visualization-2d))))))
+
+(workflow ((sequences #:type File)
+           (number-of-haplotypes #:type int
+                                 #:label "number of haplotypes")
+           ;; wfmash
+           (wfmash-chunks #:type int
+                          #:default 1
+                          #:label "number of jobs to split wfmash alignment into")
+           (segment-length #:type int
+                           #:default 1000
+                           #:label "segment seed length for mapping")
+           (block-length #:type #(int null)
+                         #:label "keep merged mappings supported by homologies of this total length (default: 5*segment_length)")
+           (map-percent-identity #:type int
+                                 #:default 90
+                                 #:label "percent identity in the mashmap step")
+           (num-mappings-for-segment #:type int
+                                     #:default 1
+                                     #:label "number of mappings to retain for each query/reference pair")
+           (no-split #:type boolean
+                     #:default #f
+                     #:label "disable splitting of input sequences during mapping")
+           (sparsify-mappings #:type #(float null)
+                              #:label "keep this fraction of mappings")
+           (kmer-size #:type int
+                      #:default 15
+                      #:label "kmer size")
+           (kmer-threshold #:type float
+                           #:default 0.001
+                           #:label "ignore the top % most-frequent kmers")
+           (exclude-delimiter #:type string
+                              #:default "#"
+                              #:label "skip mappings when the query and target have the same prefix before the last occurrence of the given character C (default assumes PanSN-spec)")
+           (hg-filter-ani-diff #:type float
+                               #:default 0.0
+                               #:label "filter out mappings unlikely to be this ANI less than the best mapping")
+           (no-merge #:type boolean
+                     #:default #f
+                     #:label "don't merge consecutive segment-level mappings")
+           ;; seqwish
+           (min-match-length #:type int
+                             #:default 23
+                             #:label "filter exact matches below this length")
+           (sparse-factor #:type float
+                          #:default 0
+                          #:label "sparsify input maches, keeping this fraction that minimizes a hash function")
+           (transclose-batch #:type string
+                             #:default "1M"
+                             #:label "number of base pairs to use for transitive closure batch")
+           ;; smoothxg
+           (consensus-prefix #:type string
+                             #:default "Consensus_"
+                             #:label "prefix of consensus path names")
+           (maximum-path-jump #:type string
+                              #:default "0"
+                              #:label "maximum path jump to include in block")
+           (maximum-edge-jump #:type string
+                              #:default "0"
+                              #:label "maximum edge jump before breaking")
+           (abpoa #:type boolean
+                  #:default #f
+                  #:label "run abPOA instead of SPOA for smoothxg")
+           (global-poa #:type boolean
+                       #:default #f
+                       #:label "run global POA alignment")
+           (poa-target-lengths #:type (array string)
+                               #:default #("700" "1100")
+                               #:label "POA target lengths; blocks are split when paths go over this length")
+           (poa-params #:type string
+                       #:default "asm20"
+                       #:label "POA score parameters")
+           (poa-padding-ratio #:type float
+                              #:default 0.001
+                              #:label "flanking sequence length fraction to pad end of each sequence with")
+           (poa-maximum-pad-depth #:type int
+                                  #:default 100
+                                  #:label "depth/haplotype at which we don't pad the POA problem")
+           (threads #:type int
+                    #:label "number of threads"))
+  (pipe (bgzip #:fasta sequences
+               #:threads threads)
+        (samtools-faidx #:compressed_fasta compressed-fasta)
+        (tee (pipe (wfmash-approximate #:sequences indexed-fasta
+                                       #:number_of_haplotypes number-of-haplotypes
+                                       #:segment_length segment-length
+                                       #:block_length block-length
+                                       #:map-percent-identity map-percent-identity
+                                       #:num-mappings-for-segment num-mappings-for-segment
+                                       #:no-split no-split
+                                       #:sparsify_mappings sparsify-mappings
+                                       #:kmer-size kmer-size
+                                       #:kmer-threshold kmer-threshold
+                                       #:exclude-delimiter exclude-delimiter
+                                       #:hg-filter-ani-diff hg-filter-ani-diff
+                                       #:no-merge no-merge
+                                       #:threads threads)
+                   (split-pairwise-alignment #:pairwise_alignment approximate-pairwise-alignment
+                                             #:chunks wfmash-chunks))
+             (identity))
+        (scatter (wfmash #:sequences indexed-fasta
+                         #:number_of_haplotypes number-of-haplotypes
+                         #:segment_length segment-length
+                         #:block_length block-length
+                         #:map-percent-identity map-percent-identity
+                         #:num-mappings-for-segment num-mappings-for-segment
+                         #:no-split no-split
+                         #:sparsify_mappings sparsify-mappings
+                         #:kmer-size kmer-size
+                         #:kmer-threshold kmer-threshold
+                         #:exclude-delimiter exclude-delimiter
+                         #:hg-filter-ani-diff hg-filter-ani-diff
+                         #:no-merge no-merge
+                         #:threads threads)
+                 #:input-paf pairwise-alignment-chunks)
+        (seqwish #:sequences sequences
+                 #:pairwise-alignments pairwise-alignment
+                 #:min-match-length min-match-length
+                 #:sparse-factor sparse-factor
+                 #:transclose-batch transclose-batch
+                 #:threads threads)
+        (rename #:unsmoothed-pangenome variation-graph)
+        (tee (pipe (smoothxg #:graph unsmoothed-pangenome
+                             #:number_of_haplotypes number-of-haplotypes
+                             #:consensus-prefix consensus-prefix
+                             #:map_percent_identity map-percent-identity
+                             #:maximum-path-jump maximum-path-jump
+                             #:maximum-edge-jump maximum-edge-jump
+                             #:abpoa abpoa
+                             #:global-poa global-poa
+                             #:poa-target-lengths poa-target-lengths
+                             #:poa_params poa-params
+                             #:poa-padding-ratio poa-padding-ratio
+                             #:poa_maximum_pad_depth poa-maximum-pad-depth
+                             #:threads threads)
+                   (reduce-redundancy #:graph smoothed-graph
+                                      #:threads threads)
+                   (tee (pipe (odgi-stats (stats-for-graph)
+                                          #:graph reduced-graph)
+                              (rename #:graph-stats stats))
+                        (visualize #:graph reduced-graph
+                                   #:ignore-prefix consensus-prefix)
+                        (visualize-2d #:graph reduced-graph
+                                      #:threads threads)
+                        (pipe (odgi-view #:graph reduced-graph)
+                              (rename #:pangenome gfa-graph))))
+             (pipe (odgi-build (build-unsmoothed-odgi-graph)
+                               #:graph unsmoothed-pangenome
+                               #:threads threads)
+                   (odgi-stats (stats-for-unsmoothed-graph)
+                               #:graph odgi-graph)
+                   (rename #:unsmoothed-graph-stats stats))
+             (identity))))