From 5ca5f9dc6ab818c26235ea78755008d63834b734 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Thu, 9 Jan 2025 11:47:03 -0700
Subject: [PATCH 1/4] PREP: add fastp & spades (moshpit)

---
 2025.4/moshpit/passed/seed-environment-conda.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/2025.4/moshpit/passed/seed-environment-conda.yml b/2025.4/moshpit/passed/seed-environment-conda.yml
index 2059d936..a989bf6d 100644
--- a/2025.4/moshpit/passed/seed-environment-conda.yml
+++ b/2025.4/moshpit/passed/seed-environment-conda.yml
@@ -7,6 +7,7 @@ dependencies:
 - biopython=1.83
 - bowtie2=2.5.1
 - entrezpy=2.1.2
+- fastp=0.24.0
 - h5py=3.11.0
 - hdf5=1.14.3
 - mafft=7.526
@@ -54,6 +55,7 @@ dependencies:
 - scipy=1.13.0
 - seaborn=0.12.2
 - sepp=4.5.5
+- spades=3.15.4
 - tqdm=4.62.3
 - umap-learn=0.5.4
 - unifrac-binaries=1.4

From e3e32405c7e400f98c9823f1a8f6fb9c60fc56cd Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Fri, 10 Jan 2025 12:28:38 -0700
Subject: [PATCH 2/4] bump spades to 4.0.0 and bump biom-format to 2.1.16

---
 2025.4/moshpit/passed/seed-environment-conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/2025.4/moshpit/passed/seed-environment-conda.yml b/2025.4/moshpit/passed/seed-environment-conda.yml
index a989bf6d..85ee708d 100644
--- a/2025.4/moshpit/passed/seed-environment-conda.yml
+++ b/2025.4/moshpit/passed/seed-environment-conda.yml
@@ -3,7 +3,7 @@ channels:
 - conda-forge
 - bioconda
 dependencies:
-- biom-format=2.1.15
+- biom-format=2.1.16
 - biopython=1.83
 - bowtie2=2.5.1
 - entrezpy=2.1.2
@@ -55,7 +55,7 @@ dependencies:
 - scipy=1.13.0
 - seaborn=0.12.2
 - sepp=4.5.5
-- spades=3.15.4
+- spades=4.0.0
 - tqdm=4.62.3
 - umap-learn=0.5.4
 - unifrac-binaries=1.4

From af21173b5c4b2de5db55e43b16ac501e6a20c84a Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Fri, 10 Jan 2025 12:29:49 -0700
Subject: [PATCH 3/4] revert biom-format bump

---
 2025.4/moshpit/passed/seed-environment-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/2025.4/moshpit/passed/seed-environment-conda.yml b/2025.4/moshpit/passed/seed-environment-conda.yml
index 85ee708d..12ea09d9 100644
--- a/2025.4/moshpit/passed/seed-environment-conda.yml
+++ b/2025.4/moshpit/passed/seed-environment-conda.yml
@@ -3,7 +3,7 @@ channels:
 - conda-forge
 - bioconda
 dependencies:
-- biom-format=2.1.16
+- biom-format=2.1.15
 - biopython=1.83
 - bowtie2=2.5.1
 - entrezpy=2.1.2

From dd4013e34e7ec39db4857df358ec1dcff0031840 Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Sat, 11 Jan 2025 00:41:04 +0000
Subject: [PATCH 4/4] Update conda environments
 (Prepare-add-fastp-spades/moshpit)

---
 .../qiime2-moshpit-macos-latest-conda.yml     | 66 ++++++++---------
 .../qiime2-moshpit-ubuntu-latest-conda.yml    | 70 +++++++++----------
 .../moshpit/passed/seed-environment-conda.yml | 46 ++++++------
 .../moshpit/staged/seed-environment-conda.yml | 48 +++++++------
 4 files changed, 115 insertions(+), 115 deletions(-)

diff --git a/2025.4/moshpit/passed/qiime2-moshpit-macos-latest-conda.yml b/2025.4/moshpit/passed/qiime2-moshpit-macos-latest-conda.yml
index 7bc42c07..038c1ddf 100644
--- a/2025.4/moshpit/passed/qiime2-moshpit-macos-latest-conda.yml
+++ b/2025.4/moshpit/passed/qiime2-moshpit-macos-latest-conda.yml
@@ -152,6 +152,7 @@ dependencies:
 - executing=2.1.0
 - expat=2.6.4
 - fastcluster=1.2.6
+- fastp=0.24.0
 - fasttree=2.1.11
 - feedparser=6.0.11
 - filelock=3.16.1
@@ -211,7 +212,7 @@ dependencies:
 - ipython=8.21.0
 - ipython_genutils=0.2.0
 - ipywidgets=8.1.5
-- isa-l=2.31.0
+- isa-l=2.31.1
 - isl=0.26
 - isoduration=20.11.0
 - jedi=0.19.2
@@ -320,7 +321,6 @@ dependencies:
 - mpc=1.3.1
 - mpfr=4.2.1
 - mpi=1.0.1
-- multimethod=1.9.1
 - munkres=1.1.4
 - muscle=3.8.1551
 - mypy_extensions=1.0.0
@@ -447,11 +447,11 @@ dependencies:
 - ptyprocess=0.7.0
 - pure_eval=0.2.3
 - pycparser=2.22
-- pydantic=2.10.4
+- pydantic=2.10.5
 - pydantic-core=2.27.2
 - pyfaidx=0.8.1.3
 - pygments=2.19.1
-- pyhmmer=0.10.15
+- pyhmmer=0.11.0
 - pyjwt=2.10.1
 - pymongo=4.10.1
 - pynacl=1.5.0
@@ -476,30 +476,30 @@ dependencies:
 - pyyaml=6.0.2
 - pyzmq=24.0.1
 - pyzotero=1.6.4
-- q2-alignment=2025.4.0.dev0+4.g06d67c6
-- q2-assembly=2025.4.0.dev0+3.g1aa29f7
-- q2-composition=2025.4.0.dev0+6.gd28ef42
-- q2-cutadapt=2025.4.0.dev0+5.g3982157
-- q2-demux=2025.4.0.dev0+4.g65f6480
-- q2-diversity=2025.4.0.dev0+6.g5170bf1
-- q2-diversity-lib=2025.4.0.dev0+4.g4d30f67
-- q2-emperor=2025.4.0.dev0+4.gb3cbec3
-- q2-feature-classifier=2025.4.0.dev0+4.g723dff9
-- q2-feature-table=2025.4.0.dev0+6.gda8969c
-- q2-fondue=2025.4.0.dev0+2.g4b1ea3e
-- q2-longitudinal=2025.4.0.dev0+4.g076c3e3
-- q2-metadata=2025.4.0.dev0+4.g089741e
-- q2-moshpit=2025.4.0.dev0+10.g077b5e5
-- q2-mystery-stew=2025.4.0.dev0+4.g61f2014
-- q2-quality-control=2025.4.0.dev0+5.g8b11caf
-- q2-quality-filter=2025.4.0.dev0+5.g42834f4
-- q2-sample-classifier=2025.4.0.dev0+4.gba6a7e8
-- q2-sapienns=2025.4.0.dev0+5.g1088a9e
+- q2-alignment=2025.4.0.dev0+5.g40a0361
+- q2-assembly=2025.4.0.dev0+5.gae9c336
+- q2-composition=2025.4.0.dev0+7.g0b19b96
+- q2-cutadapt=2025.4.0.dev0+6.g918bfe1
+- q2-demux=2025.4.0.dev0+5.g0162ce9
+- q2-diversity=2025.4.0.dev0+7.gea79f04
+- q2-diversity-lib=2025.4.0.dev0+5.g2cf3c0b
+- q2-emperor=2025.4.0.dev0+5.geb34114
+- q2-feature-classifier=2025.4.0.dev0+5.g2186a18
+- q2-feature-table=2025.4.0.dev0+7.g528f6e9
+- q2-fondue=2025.4.0.dev0+3.g43dc251
+- q2-longitudinal=2025.4.0.dev0+5.g23c62ea
+- q2-metadata=2025.4.0.dev0+5.g7af916f
+- q2-moshpit=2025.4.0.dev0+13.ga797ffb
+- q2-mystery-stew=2025.4.0.dev0+5.g51996ef
+- q2-quality-control=2025.4.0.dev0+6.gb759f55
+- q2-quality-filter=2025.4.0.dev0+6.gb7bf2b4
+- q2-sample-classifier=2025.4.0.dev0+5.gbd5055c
+- q2-sapienns=2025.4.0.dev0+6.g86ee3da
 - q2-sourmash=2025.4.0.dev0+2.ged0fedc
-- q2-taxa=2025.4.0.dev0+4.g429b1f6
-- q2-types=2025.4.0.dev0+4.gcd4ef91
-- q2-vizard=2025.4.0.dev0+84.g33eb03a
-- q2-vsearch=2025.4.0.dev0+4.g7698184
+- q2-taxa=2025.4.0.dev0+5.g0de4357
+- q2-types=2025.4.0.dev0+6.g11e14d8
+- q2-vizard=2025.4.0.dev0+85.g837033f
+- q2-vsearch=2025.4.0.dev0+5.gd7bbead
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
@@ -633,7 +633,7 @@ dependencies:
 - r-modelr=0.1.11
 - r-multcomp=1.4_26
 - r-munsell=0.5.1
-- r-mvtnorm=1.3_2
+- r-mvtnorm=1.3_3
 - r-nlme=3.1_165
 - r-nloptr=2.1.1
 - r-nnet=7.3_20
@@ -654,7 +654,7 @@ dependencies:
 - r-png=0.1_8
 - r-praise=1.0.0
 - r-prettyunits=1.2.0
-- r-processx=3.8.4
+- r-processx=3.8.5
 - r-progress=1.2.3
 - r-proxy=0.4_27
 - r-ps=1.8.1
@@ -703,7 +703,7 @@ dependencies:
 - r-sitmo=2.0.2
 - r-snow=0.4_4
 - r-sp=2.1_4
-- r-stringdist=0.9.14
+- r-stringdist=0.9.15
 - r-stringi=1.8.4
 - r-stringr=1.5.1
 - r-survival=3.8_3
@@ -731,7 +731,7 @@ dependencies:
 - r-vroom=1.6.5
 - r-waldo=0.6.1
 - r-withr=3.0.2
-- r-xfun=0.49
+- r-xfun=0.50
 - r-xml=3.99_0.17
 - r-xml2=1.3.6
 - r-xtable=1.8_4
@@ -761,7 +761,7 @@ dependencies:
 - sepp=4.5.5
 - seqtk=1.4
 - setproctitle=1.3.4
-- setuptools=75.6.0
+- setuptools=75.8.0
 - sgmllib3k=1.0.0
 - shortuuid=1.0.13
 - sigtool=0.1.3
@@ -771,7 +771,7 @@ dependencies:
 - snowballstemmer=2.2.0
 - soupsieve=2.5
 - sourmash-minimal=4.8.12
-- spades=3.15.2
+- spades=4.0.0
 - sphinx=8.1.3
 - sphinxcontrib-applehelp=2.0.0
 - sphinxcontrib-devhelp=2.0.0
diff --git a/2025.4/moshpit/passed/qiime2-moshpit-ubuntu-latest-conda.yml b/2025.4/moshpit/passed/qiime2-moshpit-ubuntu-latest-conda.yml
index b4241ff8..6e08474a 100644
--- a/2025.4/moshpit/passed/qiime2-moshpit-ubuntu-latest-conda.yml
+++ b/2025.4/moshpit/passed/qiime2-moshpit-ubuntu-latest-conda.yml
@@ -149,6 +149,7 @@ dependencies:
 - executing=2.1.0
 - expat=2.6.4
 - fastcluster=1.2.6
+- fastp=0.24.0
 - fasttree=2.1.11
 - feedparser=6.0.11
 - filelock=3.16.1
@@ -213,7 +214,7 @@ dependencies:
 - ipython=8.21.0
 - ipython_genutils=0.2.0
 - ipywidgets=8.1.5
-- isa-l=2.31.0
+- isa-l=2.31.1
 - isoduration=20.11.0
 - jedi=0.19.2
 - jinja2=3.1.5
@@ -306,7 +307,7 @@ dependencies:
 - libstdcxx=14.2.0
 - libstdcxx-devel_linux-64=14.2.0
 - libstdcxx-ng=14.2.0
-- libsystemd0=256.9
+- libsystemd0=257.2
 - libtiff=4.6.0
 - libunistring=0.9.10
 - libuuid=2.38.1
@@ -319,7 +320,6 @@ dependencies:
 - libxml2=2.12.7
 - libxslt=1.1.39
 - libzlib=1.2.13
-- llvm-openmp=8.0.1
 - llvmlite=0.42.0
 - lp_solve=5.5.2.11
 - lxml=5.2.2
@@ -343,7 +343,6 @@ dependencies:
 - mpfr=4.2.1
 - mpg123=1.32.9
 - mpi=1.0.1
-- multimethod=1.9.1
 - munkres=1.1.4
 - muscle=3.8.1551
 - mypy_extensions=1.0.0
@@ -371,7 +370,6 @@ dependencies:
 - oniguruma=6.9.10
 - openjdk=22.0.1
 - openjpeg=2.5.2
-- openmp=8.0.1
 - openssl=3.4.0
 - overrides=7.7.0
 - packaging=24.2
@@ -477,11 +475,11 @@ dependencies:
 - pulseaudio-client=17.0
 - pure_eval=0.2.3
 - pycparser=2.22
-- pydantic=2.10.4
+- pydantic=2.10.5
 - pydantic-core=2.27.2
 - pyfaidx=0.8.1.3
 - pygments=2.19.1
-- pyhmmer=0.10.15
+- pyhmmer=0.11.0
 - pyjwt=2.10.1
 - pymongo=4.10.1
 - pynacl=1.5.0
@@ -506,30 +504,30 @@ dependencies:
 - pyyaml=6.0.2
 - pyzmq=24.0.1
 - pyzotero=1.6.4
-- q2-alignment=2025.4.0.dev0+4.g06d67c6
-- q2-assembly=2025.4.0.dev0+3.g1aa29f7
-- q2-composition=2025.4.0.dev0+6.gd28ef42
-- q2-cutadapt=2025.4.0.dev0+5.g3982157
-- q2-demux=2025.4.0.dev0+4.g65f6480
-- q2-diversity=2025.4.0.dev0+6.g5170bf1
-- q2-diversity-lib=2025.4.0.dev0+4.g4d30f67
-- q2-emperor=2025.4.0.dev0+4.gb3cbec3
-- q2-feature-classifier=2025.4.0.dev0+4.g723dff9
-- q2-feature-table=2025.4.0.dev0+6.gda8969c
-- q2-fondue=2025.4.0.dev0+2.g4b1ea3e
-- q2-longitudinal=2025.4.0.dev0+4.g076c3e3
-- q2-metadata=2025.4.0.dev0+4.g089741e
-- q2-moshpit=2025.4.0.dev0+10.g077b5e5
-- q2-mystery-stew=2025.4.0.dev0+4.g61f2014
-- q2-quality-control=2025.4.0.dev0+5.g8b11caf
-- q2-quality-filter=2025.4.0.dev0+5.g42834f4
-- q2-sample-classifier=2025.4.0.dev0+4.gba6a7e8
-- q2-sapienns=2025.4.0.dev0+5.g1088a9e
+- q2-alignment=2025.4.0.dev0+5.g40a0361
+- q2-assembly=2025.4.0.dev0+5.gae9c336
+- q2-composition=2025.4.0.dev0+7.g0b19b96
+- q2-cutadapt=2025.4.0.dev0+6.g918bfe1
+- q2-demux=2025.4.0.dev0+5.g0162ce9
+- q2-diversity=2025.4.0.dev0+7.gea79f04
+- q2-diversity-lib=2025.4.0.dev0+5.g2cf3c0b
+- q2-emperor=2025.4.0.dev0+5.geb34114
+- q2-feature-classifier=2025.4.0.dev0+5.g2186a18
+- q2-feature-table=2025.4.0.dev0+7.g528f6e9
+- q2-fondue=2025.4.0.dev0+3.g43dc251
+- q2-longitudinal=2025.4.0.dev0+5.g23c62ea
+- q2-metadata=2025.4.0.dev0+5.g7af916f
+- q2-moshpit=2025.4.0.dev0+13.ga797ffb
+- q2-mystery-stew=2025.4.0.dev0+5.g51996ef
+- q2-quality-control=2025.4.0.dev0+6.gb759f55
+- q2-quality-filter=2025.4.0.dev0+6.gb7bf2b4
+- q2-sample-classifier=2025.4.0.dev0+5.gbd5055c
+- q2-sapienns=2025.4.0.dev0+6.g86ee3da
 - q2-sourmash=2025.4.0.dev0+2.ged0fedc
-- q2-taxa=2025.4.0.dev0+4.g429b1f6
-- q2-types=2025.4.0.dev0+4.gcd4ef91
-- q2-vizard=2025.4.0.dev0+84.g33eb03a
-- q2-vsearch=2025.4.0.dev0+4.g7698184
+- q2-taxa=2025.4.0.dev0+5.g0de4357
+- q2-types=2025.4.0.dev0+6.g11e14d8
+- q2-vizard=2025.4.0.dev0+85.g837033f
+- q2-vsearch=2025.4.0.dev0+5.gd7bbead
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
@@ -664,7 +662,7 @@ dependencies:
 - r-modelr=0.1.11
 - r-multcomp=1.4_26
 - r-munsell=0.5.1
-- r-mvtnorm=1.3_2
+- r-mvtnorm=1.3_3
 - r-nlme=3.1_165
 - r-nloptr=2.1.1
 - r-nnet=7.3_20
@@ -685,7 +683,7 @@ dependencies:
 - r-png=0.1_8
 - r-praise=1.0.0
 - r-prettyunits=1.2.0
-- r-processx=3.8.4
+- r-processx=3.8.5
 - r-progress=1.2.3
 - r-proxy=0.4_27
 - r-ps=1.8.1
@@ -734,7 +732,7 @@ dependencies:
 - r-sitmo=2.0.2
 - r-snow=0.4_4
 - r-sp=2.1_4
-- r-stringdist=0.9.14
+- r-stringdist=0.9.15
 - r-stringi=1.8.4
 - r-stringr=1.5.1
 - r-survival=3.8_3
@@ -762,7 +760,7 @@ dependencies:
 - r-vroom=1.6.5
 - r-waldo=0.6.1
 - r-withr=3.0.2
-- r-xfun=0.49
+- r-xfun=0.50
 - r-xml=3.99_0.17
 - r-xml2=1.3.6
 - r-xtable=1.8_4
@@ -795,7 +793,7 @@ dependencies:
 - sepp=4.5.5
 - seqtk=1.4
 - setproctitle=1.3.4
-- setuptools=75.6.0
+- setuptools=75.8.0
 - sgmllib3k=1.0.0
 - shortuuid=1.0.13
 - simplejson=3.19.3
@@ -805,7 +803,7 @@ dependencies:
 - snowballstemmer=2.2.0
 - soupsieve=2.5
 - sourmash-minimal=4.8.12
-- spades=3.15.2
+- spades=4.0.0
 - sphinx=8.1.3
 - sphinxcontrib-applehelp=2.0.0
 - sphinxcontrib-devhelp=2.0.0
diff --git a/2025.4/moshpit/passed/seed-environment-conda.yml b/2025.4/moshpit/passed/seed-environment-conda.yml
index 12ea09d9..a441b231 100644
--- a/2025.4/moshpit/passed/seed-environment-conda.yml
+++ b/2025.4/moshpit/passed/seed-environment-conda.yml
@@ -20,30 +20,30 @@ dependencies:
 - patsy=0.5.6
 - pysam=0.22.1
 - python=3.10
-- q2-alignment=2025.4.0.dev0+4.g06d67c6
-- q2-assembly=2025.4.0.dev0+3.g1aa29f7
-- q2-composition=2025.4.0.dev0+6.gd28ef42
-- q2-cutadapt=2025.4.0.dev0+5.g3982157
-- q2-demux=2025.4.0.dev0+4.g65f6480
-- q2-diversity-lib=2025.4.0.dev0+4.g4d30f67
-- q2-diversity=2025.4.0.dev0+6.g5170bf1
-- q2-emperor=2025.4.0.dev0+4.gb3cbec3
-- q2-feature-classifier=2025.4.0.dev0+4.g723dff9
-- q2-feature-table=2025.4.0.dev0+6.gda8969c
-- q2-fondue=2025.4.0.dev0+2.g4b1ea3e
-- q2-longitudinal=2025.4.0.dev0+4.g076c3e3
-- q2-metadata=2025.4.0.dev0+4.g089741e
-- q2-moshpit=2025.4.0.dev0+10.g077b5e5
-- q2-mystery-stew=2025.4.0.dev0+4.g61f2014
-- q2-quality-control=2025.4.0.dev0+5.g8b11caf
-- q2-quality-filter=2025.4.0.dev0+5.g42834f4
-- q2-sample-classifier=2025.4.0.dev0+4.gba6a7e8
-- q2-sapienns=2025.4.0.dev0+5.g1088a9e
+- q2-alignment=2025.4.0.dev0+5.g40a0361
+- q2-assembly=2025.4.0.dev0+5.gae9c336
+- q2-composition=2025.4.0.dev0+7.g0b19b96
+- q2-cutadapt=2025.4.0.dev0+6.g918bfe1
+- q2-demux=2025.4.0.dev0+5.g0162ce9
+- q2-diversity-lib=2025.4.0.dev0+5.g2cf3c0b
+- q2-diversity=2025.4.0.dev0+7.gea79f04
+- q2-emperor=2025.4.0.dev0+5.geb34114
+- q2-feature-classifier=2025.4.0.dev0+5.g2186a18
+- q2-feature-table=2025.4.0.dev0+7.g528f6e9
+- q2-fondue=2025.4.0.dev0+3.g43dc251
+- q2-longitudinal=2025.4.0.dev0+5.g23c62ea
+- q2-metadata=2025.4.0.dev0+5.g7af916f
+- q2-moshpit=2025.4.0.dev0+13.ga797ffb
+- q2-mystery-stew=2025.4.0.dev0+5.g51996ef
+- q2-quality-control=2025.4.0.dev0+6.gb759f55
+- q2-quality-filter=2025.4.0.dev0+6.gb7bf2b4
+- q2-sample-classifier=2025.4.0.dev0+5.gbd5055c
+- q2-sapienns=2025.4.0.dev0+6.g86ee3da
 - q2-sourmash=2025.4.0.dev0+2.ged0fedc
-- q2-taxa=2025.4.0.dev0+4.g429b1f6
-- q2-types=2025.4.0.dev0+4.gcd4ef91
-- q2-vizard=2025.4.0.dev0+84.g33eb03a
-- q2-vsearch=2025.4.0.dev0+4.g7698184
+- q2-taxa=2025.4.0.dev0+5.g0de4357
+- q2-types=2025.4.0.dev0+6.g11e14d8
+- q2-vizard=2025.4.0.dev0+85.g837033f
+- q2-vsearch=2025.4.0.dev0+5.gd7bbead
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
diff --git a/2025.4/moshpit/staged/seed-environment-conda.yml b/2025.4/moshpit/staged/seed-environment-conda.yml
index e60edd5c..d198d15a 100644
--- a/2025.4/moshpit/staged/seed-environment-conda.yml
+++ b/2025.4/moshpit/staged/seed-environment-conda.yml
@@ -8,6 +8,7 @@ dependencies:
 - bowtie2=2.5.1
 - busco=5.5.0
 - entrezpy=2.1.2
+- fastp=0.24.0
 - h5py=3.11.0
 - hdf5=1.14.3
 - mafft=7.526
@@ -21,31 +22,31 @@ dependencies:
 - pysam=0.22.1
 - python=3.10
 - python_abi=3.9
-- q2-alignment=2025.4.0.dev0+4.g06d67c6
-- q2-assembly=2025.4.0.dev0+3.g1aa29f7
-- q2-composition=2025.4.0.dev0+6.gd28ef42
-- q2-cutadapt=2025.4.0.dev0+5.g3982157
-- q2-demux=2025.4.0.dev0+4.g65f6480
-- q2-diversity-lib=2025.4.0.dev0+4.g4d30f67
-- q2-diversity=2025.4.0.dev0+6.g5170bf1
-- q2-emperor=2025.4.0.dev0+4.gb3cbec3
-- q2-feature-classifier=2025.4.0.dev0+4.g723dff9
-- q2-feature-table=2025.4.0.dev0+6.gda8969c
-- q2-fondue=2025.4.0.dev0+2.g4b1ea3e
-- q2-longitudinal=2025.4.0.dev0+4.g076c3e3
-- q2-metadata=2025.4.0.dev0+4.g089741e
-- q2-moshpit=2025.4.0.dev0+10.g077b5e5
-- q2-mystery-stew=2025.4.0.dev0+4.g61f2014
-- q2-quality-control=2025.4.0.dev0+5.g8b11caf
-- q2-quality-filter=2025.4.0.dev0+5.g42834f4
-- q2-sample-classifier=2025.4.0.dev0+4.gba6a7e8
-- q2-sapienns=2025.4.0.dev0+5.g1088a9e
+- q2-alignment=2025.4.0.dev0+5.g40a0361
+- q2-assembly=2025.4.0.dev0+5.gae9c336
+- q2-composition=2025.4.0.dev0+7.g0b19b96
+- q2-cutadapt=2025.4.0.dev0+6.g918bfe1
+- q2-demux=2025.4.0.dev0+5.g0162ce9
+- q2-diversity-lib=2025.4.0.dev0+5.g2cf3c0b
+- q2-diversity=2025.4.0.dev0+7.gea79f04
+- q2-emperor=2025.4.0.dev0+5.geb34114
+- q2-feature-classifier=2025.4.0.dev0+5.g2186a18
+- q2-feature-table=2025.4.0.dev0+7.g528f6e9
+- q2-fondue=2025.4.0.dev0+3.g43dc251
+- q2-longitudinal=2025.4.0.dev0+5.g23c62ea
+- q2-metadata=2025.4.0.dev0+5.g7af916f
+- q2-moshpit=2025.4.0.dev0+13.ga797ffb
+- q2-mystery-stew=2025.4.0.dev0+5.g51996ef
+- q2-quality-control=2025.4.0.dev0+6.gb759f55
+- q2-quality-filter=2025.4.0.dev0+6.gb7bf2b4
+- q2-sample-classifier=2025.4.0.dev0+5.gbd5055c
+- q2-sapienns=2025.4.0.dev0+6.g86ee3da
 - q2-sourmash=2025.4.0.dev0+2.ged0fedc
-- q2-taxa=2025.4.0.dev0+4.g429b1f6
+- q2-taxa=2025.4.0.dev0+5.g0de4357
 - q2-types-genomics=2023.11.0.dev0+8.g3b993ed
-- q2-types=2025.4.0.dev0+4.gcd4ef91
-- q2-vizard=2025.4.0.dev0+84.g33eb03a
-- q2-vsearch=2025.4.0.dev0+4.g7698184
+- q2-types=2025.4.0.dev0+6.g11e14d8
+- q2-vizard=2025.4.0.dev0+85.g837033f
+- q2-vsearch=2025.4.0.dev0+5.gd7bbead
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
@@ -57,6 +58,7 @@ dependencies:
 - scipy=1.13.0
 - seaborn=0.12.2
 - sepp=4.5.5
+- spades=4.0.0
 - tqdm=4.62.3
 - umap-learn=0.5.4
 - unifrac-binaries=1.4