Downgraded (wfmash) from 0.24 to 0.14. Pggb requires that. Cosigt tests:

● ALL 12 STEPS PASS with wfmash-0.14! And note: Step 6 now shows 142 nodes (vs 7 nodes with wfmash-0.24) -- a much more
   detailed pangenome graph from pggb with the correct wfmash version.

● Genotype: sampleA#2#chr1 + sampleC#2#chr1, cosine similarity 0.52 -- exactly matching the expected result from the
  test README!

1 files changed, 39 insertions, 42 deletions

diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 6c8e5d6..aa09df6 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -666,26 +666,6 @@ The path-guided stochastic gradient descent based 1D sort implemented in
             (lambda _
               (substitute* (find-files "scripts" "\\.py$")
                 (("/usr/bin/python") "/usr/bin/python3"))))
-          (add-after 'unpack 'fix-wfmash-flags
-            (lambda _
-              ;; wfmash 0.24 renamed/changed flags:
-              ;; --approx-map -> --approx-mapping
-              ;; -H (was hg-filter threshold) -> removed, use --hg-filter=
-              ;; --hg-filter-ani-diff N -> --hg-filter=N,0.0,99.9
-              ;; -Y DELIM (exclude-delim) -> -YDELIM (group-prefix, inline)
-              ;; --invert-filtering -> removed
-              (substitute* "pggb"
-                (("--approx-map\\b") "--approx-mapping")
-                ;; wfmash 0.24 defaults to -w 1000; pass -w = segment_length
-                ;; so short sequences aren't skipped
-                (("-l \\$block_length")
-                 "-w $segment_length -l $block_length")
-                (("-H \\$mash_kmer_thres") "")
-                (("--hg-filter-ani-diff \\$hg_filter_ani_diff")
-                 "--hg-filter=$hg_filter_ani_diff,0.0,99.9")
-                (("exclude_cmd=\"-Y \"\\$exclude_delim")
-                 "exclude_cmd=\"\"")
-                (("--invert-filtering") ""))))
           (add-after 'install 'wrap-scripts
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let ((out (assoc-ref outputs "out")))
@@ -724,34 +704,51 @@ The path-guided stochastic gradient descent based 1D sort implemented in
            seqwish
            smoothxg
            time
-           wfmash-0.24))
+           wfmash-0.14))
     (home-page "https://doi.org/10.1101/2023.04.05.535718")
     (synopsis "PanGenome Graph Builder")
     (description "pggb builds pangenome variation graphs from a set of input
 sequences using wfmash, seqwish, smoothxg, and gfaffix.")
     (license license:expat)))
 
-(define-public wfmash-0.24
+(define-public wfmash-0.14
   (package
     (inherit wfmash)
-    (name "wfmash")
-    (version "0.24.2")
+    (version "0.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
+                           version "/wfmash-v" version ".tar.gz"))
+       (sha256
+        (base32 "1mk3jschn3hdr45glds65g3hxk7v6nc3plkvxmfbd5pr4kyzlf13"))
+       (snippet
+        #~(begin
+            (use-modules (guix build utils))
+            (delete-file-recursively "src/common/atomic_queue")
+            (substitute* "src/align/include/computeAlignments.hpp"
+              (("\"common/atomic_queue/atomic_queue.h\"")
+               "<atomic_queue/atomic_queue.h>"))
+            (substitute* (find-files "." "CMakeLists\\.txt")
+              (("-march=native ") ""))))))
     (arguments
-     (list
-       #:tests? #f
-       #:configure-flags
-       #~(list "-DCMAKE_C_FLAGS=-mcx16"
-               "-DCMAKE_CXX_FLAGS=-mcx16")))
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/waveygang/wfmash/releases"
-                                  "/download/v" version
-                                  "/wfmash-v" version ".tar.gz"))
-              (sha256
-               (base32 "083nanyz0ywhh4klgymap0zjn1jyh0j7k7gxhsd03zrq4nlf91nv"))
-              (snippet
-               #~(begin
-                   (use-modules (guix build utils))
-                   (substitute* (find-files "." "CMakeLists.txt")
-                     (("-mcx16") "")
-                     (("-march=native") ""))))))))
+     (substitute-keyword-arguments (package-arguments wfmash)
+       ((#:tests? tests? #f) #f)
+       ((#:phases phases #~%standard-phases)
+        #~(modify-phases #$phases
+            (delete 'install-scripts)
+            (replace 'build-check-prerequisites
+              (lambda _
+                (let ((wfa2-lib #$(string-append "../wfmash-v"
+                                                 "0.14.0"
+                                                 "/src/common/wflign/deps/WFA2-lib")))
+                  (substitute* (string-append wfa2-lib "/Makefile")
+                    (("-march=x86-64-v3") ""))
+                  (substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
+                    (("\\\\time -v") "time"))
+                  (invoke "make" "-C" wfa2-lib
+                          #$(string-append "CC=" (cc-for-target))))))))))
+    (inputs
+     (modify-inputs (package-inputs wfmash)
+       (prepend jemalloc)
+       (delete "libdeflate")))))