From ab3ee68f5beb9a2c3086de20968492b7e090a6c9 Mon Sep 17 00:00:00 2001
From: Adrian Altenhoff <adrian.altenhoff@inf.ethz.ch>
Date: Wed, 14 Aug 2024 10:19:23 +0200
Subject: [PATCH] add step to extract taxonomy from gs_tsv

---
 containers/oma/Dockerfile                     |   9 +-
 containers/oma/Pipfile                        |   6 +-
 containers/oma/Pipfile.lock                   | 795 +++++++++---------
 modules/local/darwin_extract/main.nf          |  19 +
 .../usr/bin/subtaxonomy-from-genomes.py       |  53 ++
 subworkflows/local/extract_darwin/main.nf     |   8 +-
 6 files changed, 482 insertions(+), 408 deletions(-)
 create mode 100755 modules/local/darwin_extract/resources/usr/bin/subtaxonomy-from-genomes.py

diff --git a/containers/oma/Dockerfile b/containers/oma/Dockerfile
index 8ccd573..e1a88e6 100644
--- a/containers/oma/Dockerfile
+++ b/containers/oma/Dockerfile
@@ -1,10 +1,9 @@
-FROM python:3.11-slim as basis
+FROM python:3.11-slim AS basis
 
 # set environment varibles
-#ENV PYTHONDONTWRITEBYTECODE 1
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 
-FROM basis as builder
+FROM basis AS builder
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        build-essential \
@@ -32,7 +31,7 @@ RUN --mount=type=ssh \
     LABGIT=$(cat /run/secrets/labgit ) \
        pipenv sync
 
-FROM basis as runtime
+FROM basis AS runtime
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        libxml2 \
diff --git a/containers/oma/Pipfile b/containers/oma/Pipfile
index f2edf7f..8c3c5a6 100644
--- a/containers/oma/Pipfile
+++ b/containers/oma/Pipfile
@@ -8,9 +8,11 @@ omahdf5tordf = {git = "git+${LABGIT}/biosoda"}
 omamer = "*"
 edgehog = "*"
 hogprop = {git = "git+${LABGIT}/hogprop2"}
-         #branch = "nf-convert", 
-#pyoma = {git = "git+https://github.com/DessimozLab/pyoma.git", ref = "v0.13.3", extras = ["create_db", "enrichment", "notebooks"] }
+         #branch = "nf-convert",
+         #ref = "v0.13.3"
+#pyoma = {git = "git+https://github.com/DessimozLab/pyoma.git", branch = "nf-convert", extras = ["create_db", "enrichment", "notebooks"] }
 pyoma = "*"
+omataxonomy = "*"
 
 [dev-packages]
 
diff --git a/containers/oma/Pipfile.lock b/containers/oma/Pipfile.lock
index 31f6d3f..ed734df 100644
--- a/containers/oma/Pipfile.lock
+++ b/containers/oma/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "f566374bb92e3ba87a71f8be72593612b0b9f8ee066bb79258b480439ae4f44d"
+            "sha256": "f035926f4bdd4ca36df284e18fcd88d1f840cc1de16ef9e58ea2df71e27e1db8"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,6 +16,22 @@
         ]
     },
     "default": {
+        "about-time": {
+            "hashes": [
+                "sha256:6a538862d33ce67d997429d14998310e1dbfda6cb7d9bbfbf799c4709847fece",
+                "sha256:8bbf4c75fe13cbd3d72f49a03b02c5c7dca32169b6d49117c257e7eb3eaee341"
+            ],
+            "markers": "python_version >= '3.7' and python_version < '4'",
+            "version": "==4.2.1"
+        },
+        "alive-progress": {
+            "hashes": [
+                "sha256:347220c1858e3abe137fa0746895668c04df09c5261a13dc03f05795e8a29be5",
+                "sha256:42e399a66c8150dc507602dff7b7953f105ef11faf97ddaa6d27b1cbf45c4c98"
+            ],
+            "markers": "python_version >= '3.7' and python_version < '4'",
+            "version": "==3.1.5"
+        },
         "biopython": {
             "hashes": [
                 "sha256:0c425a39871f652598f502671aa5f6b5125475a91333a368a47f9c611ca96db1",
@@ -44,36 +60,36 @@
                 "sha256:ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae",
                 "sha256:f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_version >= '3.9'",
             "version": "==1.84"
         },
         "blosc2": {
             "hashes": [
-                "sha256:05d40ede9cf0ecb25500cfe9bebe190e75f246eb1fcd7bd358ac1acfef44ee7a",
-                "sha256:1546c04d25ce793fa0fd7a83999bbb576ff84ef474fb45801f0b6dd76b84803c",
-                "sha256:17dd39f62f1686a170232ac8bcba40358ef67e919a91fe840ac71a45d067df30",
-                "sha256:18e3c4c95fe40ea9cda88c784d96e4efc8ddf53f94074cf46daa2e91c9ae5137",
-                "sha256:3d4b208d5f5947d3062d3353717c43e0ea8e6ccdecdcd30737d5305628e0062b",
-                "sha256:407896867032a760dcce6c25d5e5a56b6fe5235245e065e2549697f69b5117c6",
-                "sha256:4518944374880d822f9ca90d4473bfa9f4d884b462f78365e224c2b291962e44",
-                "sha256:488dc4be3b6894967a7189952634644f8da46c4bab7734719d379cdf5b440dc0",
-                "sha256:565701ad336946a7ef12250def97aae2257de1da34ac8cd570be91b664a03d30",
-                "sha256:5b640fe2d1d39af2dccffe5e100ef94d21940bfb7f0af44ba17fef718671b267",
-                "sha256:62d2a6eaf1be1858993a4d7b2b8efd2ede5c4eaabe030c611cd075d907aa5400",
-                "sha256:634bc22f17ae47a166b8201c77ba11bc160d9997ace51fc820cb3cbd285d47f8",
-                "sha256:64a26c9f7a4a5ddc5721a75b37f913f9e21c0dab96d8c152a64f8faf8659e9ee",
-                "sha256:729305b06e76b0c95b0ea5090aa7ec87eff72ca43e194283e0cccee92bbdd1e6",
-                "sha256:770733ce68d82674d1f80961fe56f3c2d914d8ea4de036af3888a22479add97d",
-                "sha256:928a89851b8528ce9c233048d832be5b2fef47645d5a389c021f3f58333fa3f8",
-                "sha256:9b982c1d40560eefb4a01d67c57e786d39a5ee9696f3deadd32ebf5f8885eb2a",
-                "sha256:a9518b7bbaa0f9903a5a921abe6abb0faa56b0e0ad2da0416ff3a486a4b2e0aa",
-                "sha256:aa71042277956199676169335eb64aa76e33adac5a22289eccdb7d10edf402b6",
-                "sha256:b1ac66ce25214b0b2e53beda9bc6f333dba16f2667649b1026ae041511b5a07d",
-                "sha256:c6a700f9324b37e814c5633c43b081c60962f4dd59c0340cefe5f61f9f0411fd",
-                "sha256:fd3ca9a61bce4e4dc8006b613fa9dd8982f71e01fa9f593d6cc44d9fdbb56174"
+                "sha256:06e0933855a6cba347692f08de1aaa51a8858dda67e7c5eaeaab59663b897879",
+                "sha256:150030e81bd5037f802ce7844281a37ff67e0998aa1735c48b02f3c6401bf0a1",
+                "sha256:18770f75174a3aae5712f53e9cb5885b258b730b281cbb3bf1e7a74ea3d94fae",
+                "sha256:23763b3602df9b0e63d16d21abadaac426a74370a0a986f08bf5322bcfd207c6",
+                "sha256:2c7dbdd93378d01b048536b2eccbb77eaa73054665bc3a9396e4e391a50c4ad0",
+                "sha256:3412e83e6b2508f3da0b0f3e0bf86bef4dac56f018525d2ab55ca50712a2b91a",
+                "sha256:34db4d41543b16e894d507d6c7d10a9a67c9dd420ff40b072f7c39185cbb8fe8",
+                "sha256:3c10a9505c6d2d5e58f03a1139b4a4b234511baa9ebeba17f8f1cc22881ca764",
+                "sha256:51fa45187639cd1f7822355c91f6ceb0fbff6157eb6f9c32462782551fc61283",
+                "sha256:5923a22fb7cfdad571b316930e8812618ba8b2ac1f37ac05edcf3eda71beed9f",
+                "sha256:6c1f3e5ed25930596492dddac8022a729d538efb3c1c4e4904a0021288cf4835",
+                "sha256:6c894ef42fabc49c6bd1c41d2e45ac24e911b3b711c1e26f9be93dbcbf5fd4e2",
+                "sha256:7a369a72467b54fb45aa307cf6e3ae84ec0212a9b55cfa5f4d4eb06a06bb1472",
+                "sha256:9b00bcaeaf125491cc6dec5508389f95152de69cc678a63a0310a756511f3d21",
+                "sha256:a1a884f181a2a9612470bcd589794c7adda3eebdaed918e1a8b6e69683524b70",
+                "sha256:ad698c6fca8dee677b7a1881206f7ac43ffd7c458733716a3de1e1f3c6ba1f79",
+                "sha256:bd91a5d9e1d35b47bf5a3b6b440bc120f1fa0af45264c0a6ccca6b1083de43e9",
+                "sha256:bf55816beaf34eaba021904ee7d6c428ca338d0f3ec7a5be04dda552258d0a8b",
+                "sha256:c662a3cab4760c194407de1990bd70608af29ee30d6471072463cdc8cc6586c4",
+                "sha256:d5e03ec783841c82ba6704638f5847a80cac8625186932a8f3b47bc5fbda4f7e",
+                "sha256:ed15f0eb6a99df425b33be948fb309a97e76bda37eae20022bc9611bce775592",
+                "sha256:f8134aaaf72b670f2ddf258d9b64646c262d6b1b112a530d39f9a5d316f3b306"
             ],
             "markers": "python_version >= '3.10' and python_version < '4'",
-            "version": "==2.7.0"
+            "version": "==2.7.1"
         },
         "certifi": {
             "hashes": [
@@ -179,70 +195,6 @@
             "markers": "python_full_version >= '3.7.0'",
             "version": "==3.3.2"
         },
-        "cython": {
-            "hashes": [
-                "sha256:051069638abfb076900b0c2bcb6facf545655b3f429e80dd14365192074af5a4",
-                "sha256:076e9fd4e0ca33c5fa00a7479180dbfb62f17fe928e2909f82da814536e96d2b",
-                "sha256:077b61ee789e48700e25d4a16daa4258b8e65167136e457174df400cf9b4feab",
-                "sha256:09f2000041db482cad3bfce94e1fa3a4c82b0e57390a164c02566cbbda8c4f12",
-                "sha256:0bac3ccdd4e03924028220c62ae3529e17efa8ca7e9df9330de95de02f582b26",
-                "sha256:0e9a885ec63d3955a08cefc4eec39fefa9fe14989c6e5e2382bd4aeb6bdb9bc3",
-                "sha256:15b6d397f4ee5ad54e373589522af37935a32863f1b23fa8c6922adf833e28e2",
-                "sha256:206e803598010ecc3813db8748ed685f7beeca6c413f982df9f8a505fce56563",
-                "sha256:269f06e6961e8591d56e30b46e1a51b6ccb42cab04c29fa3b30d3e8723485fb4",
-                "sha256:2c9c1e3e78909488f3b16fabae02308423fa6369ed96ab1e250807d344cfffd7",
-                "sha256:2d29e617fd23cf4b83afe8f93f2966566c9f565918ad1e86a4502fe825cc0a79",
-                "sha256:32fbad02d1189be75eb96456d9c73f5548078e5338d8fa153ecb0115b6ee279f",
-                "sha256:35f6ede7c74024ed1982832ae61c9fad7cf60cc3f5b8c6a63bb34e38bc291936",
-                "sha256:38d40fa1324ac47c04483d151f5e092406a147eac88a18aec789cf01c089c3f2",
-                "sha256:3919a55ec9b6c7db6f68a004c21c05ed540c40dbe459ced5d801d5a1f326a053",
-                "sha256:3cffb666e649dba23810732497442fb339ee67ba4e0be1f0579991e83fcc2436",
-                "sha256:401aba1869a57aba2922ccb656a6320447e55ace42709b504c2f8e8b166f46e1",
-                "sha256:407840c56385b9c085826fe300213e0e76ba15d1d47daf4b58569078ecb94446",
-                "sha256:40fac59c3a7fbcd9c25aea64c342c890a5e2270ce64a1525e840807800167799",
-                "sha256:4f610964ab252a83e573a427e28b103e2f1dd3c23bee54f32319f9e73c3c5499",
-                "sha256:4fadb84193c25641973666e583df8df4e27c52cdc05ddce7c6f6510d690ba34a",
-                "sha256:541fbe725d6534a90b93f8c577eb70924d664b227a4631b90a6e0506d1469591",
-                "sha256:5a036d00caa73550a3a976432ef21c1e3fa12637e1616aab32caded35331ae96",
-                "sha256:5bd49a3a9fdff65446a3e1c2bfc0ec85c6ce4c3cad27cd4ad7ba150a62b7fb59",
-                "sha256:5f465443917d5c0f69825fca3b52b64c74ac3de0143b1fff6db8ba5b48c9fb4a",
-                "sha256:64f1f8bba9d8f37c0cffc934792b4ac7c42d0891077127c11deebe9fa0a0f7e4",
-                "sha256:651a15a8534ebfb9b58cb0b87c269c70984b6f9c88bfe65e4f635f0e3f07dfcd",
-                "sha256:6c5af936940a38c300977b81598d9c0901158f220a58c177820e17e1774f1cf1",
-                "sha256:712760879600907189c7d0d346851525545484e13cd8b787e94bfd293da8ccf0",
-                "sha256:81f356c1c8c0885b8435bfc468025f545c5d764aa9c75ab662616dd1193c331e",
-                "sha256:86998b01f6a6d48398df8467292c7637e57f7e3a2ca68655367f13f66fed7734",
-                "sha256:8adcde00a8a88fab27509b558cd8c2959ab0c70c65d3814cfea8c68b83fa6dcd",
-                "sha256:8c9c4c4f3ab8f8c02817b0e16e8fa7b8cc880f76e9b63fe9c010e60c1a6c2b13",
-                "sha256:8f2864ab5fcd27a346f0b50f901ebeb8f60b25a60a575ccfd982e7f3e9674914",
-                "sha256:90e2f514fc753b55245351305a399463103ec18666150bb1c36779b9862388e9",
-                "sha256:950c0c7b770d2a7cec74fb6f5ccc321d0b51d151f48c075c0d0db635a60ba1b5",
-                "sha256:9cc6a0e7e23a96dec3f3c9d39690d4281beabd5297855140d0d30855f950275e",
-                "sha256:9ea31184c7b3a728ef1f81fccb161d8948c05aa86c79f63b74fb6f3ddec860ec",
-                "sha256:9fa9e7786083b6aa61594c16979d621b62e61fcd9c2edd4761641b95c7fb34b2",
-                "sha256:a181144c2f893ed8e6a994d43d0b96300bc99873f21e3b7334ca26c61c37b680",
-                "sha256:a5e14a8c6a8157d2b0cdc2e8e3444905d20a0e78e19d2a097e89fb8b04b51f6b",
-                "sha256:a9bb402674788a7f4061aeef8057632ec440123e74ed0fb425308a59afdfa10e",
-                "sha256:a9c976e9ec429539a4367cb4b24d15a1e46b925976f4341143f49f5f161171f5",
-                "sha256:acfbe0fff364d54906058fc61f2393f38cd7fa07d344d80923937b87e339adcf",
-                "sha256:adc377aa33c3309191e617bf675fdbb51ca727acb9dc1aa23fc698d8121f7e23",
-                "sha256:b74b700d6a793113d03fb54b63bdbadba6365379424bac7c0470605672769260",
-                "sha256:bcc9795990e525c192bc5c0775e441d7d56d7a7d02210451e9e13c0448dba51b",
-                "sha256:d092c0ddba7e9e530a5c5be4ac06db8360258acc27675d1fc86294a5dc8994c5",
-                "sha256:d10fc9aa82e5e53a0b7fd118f9771199cddac8feb4a6d8350b7d4109085aa775",
-                "sha256:d4e83a8ceff7af60064da4ccfce0ac82372544dd5392f1b350c34f1b04d0fae6",
-                "sha256:dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99",
-                "sha256:e876272548d73583e90babda94c1299537006cad7a34e515a06c51b41f8657aa",
-                "sha256:e8df79b596633b8295eaa48b1157d796775c2bb078f32267d32f3001b687f2fd",
-                "sha256:f43a58bf2434870d2fc42ac2e9ff8138c9e00c6251468de279d93fa279e9ba3b",
-                "sha256:f4780d0f98ce28191c4d841c4358b5d5e79d96520650910cd59904123821c52d",
-                "sha256:f8a2b8fa0fd8358bccb5f3304be563c4750aae175100463d212d5ea0ec74cbe0",
-                "sha256:fc6e0faf5b57523b073f0cdefadcaef3a51235d519a0594865925cadb3aeadf0",
-                "sha256:fcbb679c0b43514d591577fd0d20021c55c240ca9ccafbdb82d3fb95e5edfee2"
-            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==3.0.10"
-        },
         "datasketch": {
             "hashes": [
                 "sha256:59311b2925b2f37536e9f7c2f46bbc25e8e54379c8635a3fa7ca55d2abb66d1b",
@@ -260,12 +212,12 @@
         },
         "edgehog": {
             "hashes": [
-                "sha256:6975b59b7f4e4b92b55b844e4169eeeb59866edac6d5b5dc4d000660aa7c065c",
-                "sha256:a557ae34cadd1fb273d5a25406550413549a038602df620fa59812b3b3a95d11"
+                "sha256:5090e8841f3f4d14b2a38fa0904a3e682890d591bab795a26f41645d3e4c34c8",
+                "sha256:ea026e68c07b7512d3027aa5f1b5b6b504d48c65073c27cd458d61c19b54553b"
             ],
             "index": "pypi",
             "markers": "python_version >= '3.10' and python_version < '3.13'",
-            "version": "==0.1.4"
+            "version": "==0.1.5"
         },
         "ete3": {
             "hashes": [
@@ -313,6 +265,12 @@
             "markers": "python_version >= '3.6'",
             "version": "==0.2.4"
         },
+        "grapheme": {
+            "hashes": [
+                "sha256:44c2b9f21bbe77cfb05835fec230bd435954275267fea1858013b102f8603cca"
+            ],
+            "version": "==0.6.0"
+        },
         "h5py": {
             "hashes": [
                 "sha256:083e0329ae534a264940d6513f47f5ada617da536d8dccbafc3026aefc33c90e",
@@ -396,151 +354,147 @@
         },
         "lxml": {
             "hashes": [
-                "sha256:02437fb7308386867c8b7b0e5bc4cd4b04548b1c5d089ffb8e7b31009b961dc3",
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-                "sha256:06668e39e1f3c065349c51ac27ae430719d7806c026fec462e5693b08b95696b",
-                "sha256:07542787f86112d46d07d4f3c4e7c760282011b354d012dc4141cc12a68cef5f",
-                "sha256:08ea0f606808354eb8f2dfaac095963cb25d9d28e27edcc375d7b30ab01abbf6",
-                "sha256:0969e92af09c5687d769731e3f39ed62427cc72176cebb54b7a9d52cc4fa3b73",
-                "sha256:0a028b61a2e357ace98b1615fc03f76eb517cc028993964fe08ad514b1e8892d",
-                "sha256:0b3f5016e00ae7630a4b83d0868fca1e3d494c78a75b1c7252606a3a1c5fc2ad",
-                "sha256:13e69be35391ce72712184f69000cda04fc89689429179bc4c0ae5f0b7a8c21b",
-                "sha256:16a8326e51fcdffc886294c1e70b11ddccec836516a343f9ed0f82aac043c24a",
-                "sha256:19b4e485cd07b7d83e3fe3b72132e7df70bfac22b14fe4bf7a23822c3a35bff5",
-                "sha256:1a2569a1f15ae6c8c64108a2cd2b4a858fc1e13d25846be0666fc144715e32ab",
-                "sha256:1a7aca7964ac4bb07680d5c9d63b9d7028cace3e2d43175cb50bba8c5ad33316",
-                "sha256:1b590b39ef90c6b22ec0be925b211298e810b4856909c8ca60d27ffbca6c12e6",
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@@ -614,11 +568,11 @@
         },
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@@ -730,12 +684,21 @@
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@@ -747,36 +710,38 @@
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@@ -802,12 +767,12 @@
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+                "sha256:9f469dbc9c4aeaac7dd005992af74b7dff94aa56a3ea063ce64e4b3e6736dd2f",
+                "sha256:a0cb157162f0cdd62e538c7bd298ff669847fc43a96422811d5ab933f4c16c3a",
+                "sha256:a1e037fb89f714a220f68f902fc6300ab7a33349f3ce8ffae668c3b3a40b0b06",
+                "sha256:a657eee4b94668faf1fa2703bdd803654303f7e468eb9ba10a664d867ed9e779",
+                "sha256:a65c2f63218ea2dedd56fc56361035e189ca123bd9c9ce63a9bef6f99540d681",
+                "sha256:a7a03da59b6c7c97e657dd5cd4bcaab5fe4a2affd8193958d6f4d938bee36679",
+                "sha256:a7ed0d0b9c85720f0ae33ac5efc8dc3f60c1489dad5c29d735fbdf2f66f0431f",
+                "sha256:a9ed7ad9adb68d0fe63a156fe752bbf5f1403ed66961551e749641af2874da92",
+                "sha256:ad9462aa2be9f60b540c19a083471fdf28e7cf6434f068b631525b5e6251b35e",
+                "sha256:aed13e5edacb0ecadcc304cc66e93e7e77ff24f059c9792ee602c0381808e10c",
+                "sha256:af26ebd3714224fbf9bebbc27bdbac14f334c15f5d7043699cd694635050d6ca",
+                "sha256:af440e36b828922256d0b4d79443bf2cbe5515fc4b0e9e96017ec789b36bb9fc",
+                "sha256:b6b8dd4af6324fc325d9483bec75ecf9be33e590928c9202d408e4eafff6a0a6",
+                "sha256:b8ca862927a0b05bd825e46ddf82d0724ea44b07d898ef639386530bf9b40f15",
+                "sha256:c18897c95c0a288347e29537b63608a8f63a5c3cb6da258ac46fcf89155e723e",
+                "sha256:c256fa95d29cbe5aa717db790b231a9a5b49e5983d50dc9df29d364a1db5e35b",
+                "sha256:c4e86c2b3827fa6169ad6e7d4b790ce02a20acefb8b78d92fa4249589bbc7a2c",
+                "sha256:c608fcba8b14d86c04cb56b203fed31a96e8a1ebb4ce99e7b70313c5bf8cf497",
+                "sha256:c6254c50f15bc2fcc33cb93a95a81b702d9e6590f432a7f7822b8c7aba9ae288",
+                "sha256:cc7a0d4b2cb166bc46d02c8c9f7551cde8e2f3c9789df3827309433ee9771163",
+                "sha256:ccd1763b608fb4629a0b08f00b3c099d6395e67c14e619f6341b2c8429c2f310",
+                "sha256:ce2bce52b5c150878e558a0418c2b637fb3dbb6eb38e4eb27d24aa839920483e",
+                "sha256:d214e063bffa13e3b771520b74f674b22d309b5720d4df9918ff3e0c0f037720",
+                "sha256:d41c00ded0e22e9dba88ff23ebe0dc9d2a5f21ba2f88e185ea7374461e61daa9",
+                "sha256:d50acc0e9d67e4ba7a004a14c42d1b1e8b6ca1c515692746f4f8e7948c673167",
+                "sha256:d97d3c9d209d5c30172baea5966f2129e8a198fec4a1aeb2f92abb6e82a2edb1",
+                "sha256:e03fdf0e74f346ed7e798135df5f2a0fb8d6b96582b00ebef202dcf2171e1d1d",
+                "sha256:e3a4244f65dbc3580b1275480118c3763f9dc29fc3dd96610560cb5e140a4d4a",
+                "sha256:ece873c093aedd87fc07c2a7e333d52e458dc177016afa1edaf157e82b6914d8",
+                "sha256:ed443a2062460f44c0346cb9d269b586496b808c2419bbd6057f54061c9b9c75",
+                "sha256:ee2d8355c7343c631a03e57540ea06e8717c19ecf5ff64ea07e0498f7f161457",
+                "sha256:efa674b407424553024522159296690d99d6e6b1192cafe99ca84592faff16b4",
+                "sha256:f3deff6ab7017ed21b9aec5874a07ad13e6b2a688af055837f88b743c7bfd947",
+                "sha256:f3f42504bdc8d770987fc3d99964766d42b2a03e4d5b0f891decdd256236bae0",
+                "sha256:f6ebb910a702e41641e1e1dada3843bc11ba9107a33c98daef6945a885a40a07",
+                "sha256:f6f0256cb27b6a0fb2e1918477d1b56473cd04acfa245376a342e7c15806a396",
+                "sha256:f982e1aafb4bd8207a5e073b1efef9e68a984e91330e1bbf364f9ed157ed83f0",
+                "sha256:fa742ec60bec53c5a211632cf1d31b9eb5a3c80f1371a46a23ac25a1fa2ab209",
+                "sha256:fb5a514064e02585b1cc09da2fe406a6dc1a7e5f3e92dd4f27c53e5f1465ec81"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==3.9.5"
+            "version": "==3.9.6"
         },
         "rdflib": {
             "hashes": [
@@ -981,6 +955,12 @@
             "markers": "python_version >= '3.8'",
             "version": "==2.32.3"
         },
+        "rmath4": {
+            "hashes": [
+                "sha256:c39a75e1c883fd6f5d6b6677213b4e0704ce014f060d0d00b89f5ff608b72300"
+            ],
+            "version": "==4.3.1"
+        },
         "scipy": {
             "hashes": [
                 "sha256:076c27284c768b84a45dcf2e914d4000aac537da74236a0d45d82c6fa4b7b3c0",
@@ -1014,11 +994,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1",
-                "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"
+                "sha256:80aacbf633704e9c8bfa1d99fa5dd4dc59573efcf9e4042c13d3bcef91ac2ef9",
+                "sha256:f11dd94b7bae3a156a95ec151f24e4637fb4fa19c878e4d191bfb8b2d82728c4"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==72.1.0"
+            "version": "==72.2.0"
         },
         "six": {
             "hashes": [
@@ -1030,34 +1010,49 @@
         },
         "tables": {
             "hashes": [
-                "sha256:164b945d0cb731c7232775fd3657f150bcf05413928b86033b023a1dc8dbeb05",
-                "sha256:2848fb3dce30a7b83fa099d026a91d7b10ad48afae04fa10f974f1da3f1e2bbf",
-                "sha256:5fbea426ce9bdd60cda435a265823b31d18f2b36e9045fb2d565679825a7aa46",
-                "sha256:8a4e71fc9d2a3a0cacce4994afd47cd5f4797093ff9cee2cc7dc87e51f308107",
-                "sha256:8e67c71070b871fade3694a4c764504e03836bb1843321766cf2e40b7d280e84",
-                "sha256:9d6bbc477d038a17c5062ab6ccd94c8b1fa365cf017b9a2ad6c2dff1a07abb2b",
-                "sha256:a068d4ad08d5a6b2ad457f60ac6676efdab9e29459e776e433d5537a46e62e41",
-                "sha256:ab9291ff4d243e7966b6706a2675b83138bd9bbe82721d695b78971660d59632",
-                "sha256:b131c9b4e003816a45e2efe5c5c797d01d8308cac4aee72597a15837cedb605c",
-                "sha256:bca5a6bf162a84a6ef74ca4017b28c59c1526cffdbd93ce94c98ff8f9593f1d5",
-                "sha256:c14dc879b041cf53be1afe9e5ed581e1aeacdcee9e2e1ee79110dc96a4c8d97c",
-                "sha256:c52087ed8b90a5f6ba87f0adcd1c433e5f5db7c7ca5984b08ff45f2247635f7d",
-                "sha256:c6304d321452fd56865e5c309e38373011b0f0f6c714786c5660613ceb623acb",
-                "sha256:d470263c2e50c4b7c8635a0d99ac1ff2f9e704c24d71e5fa33c4529e7d0ad9c3",
-                "sha256:d71913fb8147dc6132595b94fc82f88f6c2436a3b5c57aadfe26c680f96aa387",
-                "sha256:e756c272bb111d016fec1d03a60095403a8fb42a5fbaf5f317dcf6e3b9d8e92e",
-                "sha256:eea41cb32dd22b30d6f3dd4e113f6d693384d301c89f3c4b4712f90c9c955875"
+                "sha256:0dcb80e6137805174c79a1dc82cad303d9600431189510eaff3de11b30afe22f",
+                "sha256:29bf223e9e3bc8d0198cbcee4d35f0ce56106c31375ce7db3da27fb13755119e",
+                "sha256:318570741040a2480c842a70978990433143a0b4b550ae6f9facab67495c16e9",
+                "sha256:3a22fc0e478d3d9bb19291a4a985a247fedb0f36a09b0ca12167c13cb07f0874",
+                "sha256:491647fb4c22535fbe373f66da6351537a5c8c2c4680b9fbde49d5e9c0c7e2e0",
+                "sha256:51edb9411a3f780efaca5291dd5447fecb6886f4363e2e0a37de1373b2f5ad10",
+                "sha256:71901560155dae3cea93d6bc624a879213da09f64d0530e748df0525759656a8",
+                "sha256:73f8de747a49b57699b398eff1c33bb7492ec961bbd7820664ba0b8073ecba3c",
+                "sha256:8fb62f3b45582adeddec8cf10c7f3128d9115ab02cdead26ca635dba1f1429a9",
+                "sha256:996b67fa54eee0365285ed3670824ad90d3f453adbbb3b68b9aff4df7aa57bed",
+                "sha256:a26963cd4410f9f3ac88ca2f8bd300f3d381ec8fd2e82300a7f50691c7688222",
+                "sha256:b84432d17a408ad1408cf4683cc39218566267a2872ee24758a9ec555d455779",
+                "sha256:cbc981a4ff8653f1b8800a6fbdc59f999294a543187452f119c98861815c64e4",
+                "sha256:db25816164550b7b1634fa669577c40ab1ebaca9f718f5813daf33f39d564d5d",
+                "sha256:f8fa4b49012bbd4706a4708ff47ec1428a6d3deeba404205bcdf1179c6b2b864",
+                "sha256:fefb61fbc3185804b45cb134a6ea6b09c9c906b8ddbe1d130e9667c9ecd5f183"
             ],
-            "markers": "python_version >= '3.9'",
-            "version": "==3.9.2"
+            "markers": "python_version >= '3.10'",
+            "version": "==3.10.0"
         },
         "tqdm": {
             "hashes": [
-                "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644",
-                "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"
+                "sha256:90279a3770753eafc9194a0364852159802111925aa30eb3f9d85b0e805ac7cd",
+                "sha256:e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==4.66.4"
+            "version": "==4.66.5"
+        },
+        "typing-extensions": {
+            "hashes": [
+                "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d",
+                "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==4.12.2"
+        },
+        "tzdata": {
+            "hashes": [
+                "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd",
+                "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"
+            ],
+            "markers": "python_version >= '2'",
+            "version": "==2024.1"
         },
         "urllib3": {
             "hashes": [
diff --git a/modules/local/darwin_extract/main.nf b/modules/local/darwin_extract/main.nf
index 849f861..8106e25 100644
--- a/modules/local/darwin_extract/main.nf
+++ b/modules/local/darwin_extract/main.nf
@@ -55,3 +55,22 @@ process CONVERT_PROTEINS {
         EOF
         """
 }
+
+process CONVERT_TAXONOMY {
+    tag "Convert Taxonomy of genomes using omataxonomy"
+    label "process_single"
+    container "dessimozlab/omabuild:nf-latest"
+
+    input:
+        path gs_tsv
+        path sqlite_taxonomy
+
+    output:
+        path "taxonomy.tsv",          emit: tax_tsv
+
+    script:
+        """
+        python subtaxonomy-from-genomes.py --input $gs_tsv --database $sqlite_taxonomy --out taxonomy.tsv
+
+        """
+}
diff --git a/modules/local/darwin_extract/resources/usr/bin/subtaxonomy-from-genomes.py b/modules/local/darwin_extract/resources/usr/bin/subtaxonomy-from-genomes.py
new file mode 100755
index 0000000..7a45f2a
--- /dev/null
+++ b/modules/local/darwin_extract/resources/usr/bin/subtaxonomy-from-genomes.py
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+
+import omataxonomy
+import csv
+
+def subtaxonomy_from_genomes(tax, genomes):
+    tree = tax.get_topology(genomes.keys(), intermediate_nodes=True, collapse_subspecies=True, annotate=True)
+    taxtab = []
+    while True:
+        if len(tree.children) != 1: break
+        tree = tree.children[0]
+
+    for node in tree.traverse(strategy="preorder"):
+        parent_taxid = node.up.taxid if node.up is not None and node != tree else -1
+        if node.taxid in (131567, 1):
+            node.taxid = 0
+            sciname = "LUCA"
+        elif node.sci_name.startswith("d__"):
+            sciname = node.sci_name.replace("d__", "")
+            node.taxid = tax.get_name_translator([sciname])[sciname][0]
+        else:
+            sciname = node.sci_name
+            if node.taxid in genomes:
+                sciname = genomes[node.taxid]
+        if node.taxid == parent_taxid:
+            continue
+        taxtab.append((node.taxid, parent_taxid, sciname))
+    return taxtab
+
+
+def parse_genomes_tsv(genomes_tsv):
+    with open(genomes_tsv, 'r') as f:
+        dialect = csv.Sniffer().sniff(f.read(1000))
+        f.seek(0)
+        reader = csv.DictReader(f, dialect=dialect)
+        genomes = {int(row['TaxonId']): row['SciName'] for row in reader}
+    return genomes
+
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser(description="Extract a subtaxonomy from a set of genomes")
+    parser.add_argument('--input', required=True, help="Genomes file in TSV format")
+    parser.add_argument('--database', help="Taxonomy database file (sqlite format)")
+    parser.add_argument('--out', required=True, help="Path to output file")
+    conf = parser.parse_args()
+
+    tax = Taxonomy(conf.database)
+    genomes = parse_genomes_tsv(conf.input)
+    taxtab = subtaxonomy_from_genomes(tax, genomes)
+
+    with open(conf.out, 'w') as f:
+        csv.writer(f, dialect="excel-tab").writerows(taxtab)
diff --git a/subworkflows/local/extract_darwin/main.nf b/subworkflows/local/extract_darwin/main.nf
index 9265be6..c04d150 100644
--- a/subworkflows/local/extract_darwin/main.nf
+++ b/subworkflows/local/extract_darwin/main.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 // Modules
-include { CONVERT_GS; CONVERT_PROTEINS } from "./../../../modules/local/darwin_extract"
+include { CONVERT_GS; CONVERT_PROTEINS; CONVERT_TAXONOMY } from "./../../../modules/local/darwin_extract"
 
 workflow EXTRACT_DARWIN {
     take:
@@ -11,6 +11,7 @@ workflow EXTRACT_DARWIN {
 
     main:
         def summaries = genomes_folder / "Summaries.drw"
+        def taxonomy = genomes_folder / "taxonomy.sqlite"
         CONVERT_GS(genomes_folder, matrix_file, summaries)
         CONVERT_GS.out.gs_tsv
             | splitCsv(sep: "\t", header: true)
@@ -22,8 +23,13 @@ workflow EXTRACT_DARWIN {
             | set { convert_jobs }
         CONVERT_PROTEINS(convert_jobs)
 
+        CONVERT_TAXONOMY(CONVERT_GS.out.gs_tsv, taxonomy)
+
+
     emit:
         gs_file = CONVERT_GS.out.gs_tsv
         protein_files = CONVERT_PROTEINS.out.prot_json.collect()
+        tax_tsv = CONVERT_TAXONOMY.out.tax_tsv
+
 }