From 68a9f303269d1c1784f4b94e3fc8d25ee8055883 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Mon, 23 Mar 2026 23:14:34 +0000
Subject: Initial commit
---
COPYING | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
README.md | 36 ++++
channels.scm | 25 +++
manifest.scm | 41 ++++
pggb.scm | 506 ++++++++++++++++++++++++++++++++++++++++++++
5 files changed, 1282 insertions(+)
create mode 100644 COPYING
create mode 100644 README.md
create mode 100644 channels.scm
create mode 100644 manifest.scm
create mode 100644 pggb.scm
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..f288702
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
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+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.
+
+
+ Copyright (C)
+
+ 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 .
+
+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:
+
+ Copyright (C)
+ 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
+.
+
+ 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
+.
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
+;;;
+;;; 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 .
+
+;;;
+;;; 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))))
--
cgit 1.4.1