merge_updated_branches_from_main_repo#1
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…6ee6e0ad164b238136e2f618fa5b31-af6eea407d408c9459ae19ad447137ff11ab989f Add container mulled-v2-1c7ead01006ee6e0ad164b238136e2f618fa5b31:af6eea407d408c9459ae19ad447137ff11ab989f.
…ac817c2eeb6b0df6c70a618ff952d6-82790c27cd80ce7b1fef4f77bad70398f9fe3900 Add container mulled-v2-a5123547e1ac817c2eeb6b0df6c70a618ff952d6:82790c27cd80ce7b1fef4f77bad70398f9fe3900.
…c0467aa04a1608cfd59d6164ace5f8dd7dbb. **Hash**: mulled-v2-d3567f5619929c65634ae5e58d309a2d5e1103f3:8cb4c0467aa04a1608cfd59d6164ace5f8dd7dbb **Packages**: - perl-math-cdf=0.1 - ensembl-vep=115 - grep=3.11 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - ensembl_vep.xml Generated with Planemo.
…abd7791103627626559e2040833490206e65. **Hash**: mulled-v2-1bd7c143fec0659638fb990d05ec2cc030bd8b61:5e5fabd7791103627626559e2040833490206e65 **Packages**: - coreprofiler=1.1.4 - blast=2.16.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - data_manager_build_coreprofiler_download.xml Generated with Planemo.
…c0659638fb990d05ec2cc030bd8b61-5e5fabd7791103627626559e2040833490206e65 Add container mulled-v2-1bd7c143fec0659638fb990d05ec2cc030bd8b61:5e5fabd7791103627626559e2040833490206e65.
…929c65634ae5e58d309a2d5e1103f3-8cb4c0467aa04a1608cfd59d6164ace5f8dd7dbb Add container mulled-v2-d3567f5619929c65634ae5e58d309a2d5e1103f3:8cb4c0467aa04a1608cfd59d6164ace5f8dd7dbb.
…12e18332de5a030bf1ab1353c17d8448cd90. **Hash**: mulled-v2-f44eb8f8fd694df8f5d103351c6e7f6816bd9bb1:a06a12e18332de5a030bf1ab1353c17d8448cd90 **Packages**: - sed=4.9 - grep=3.11 - coreutils=9.5 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - sorter.xml Generated with Planemo.
…694df8f5d103351c6e7f6816bd9bb1-a06a12e18332de5a030bf1ab1353c17d8448cd90 Add container mulled-v2-f44eb8f8fd694df8f5d103351c6e7f6816bd9bb1:a06a12e18332de5a030bf1ab1353c17d8448cd90.
Rebuild snpeff,gawk container to capture snpeff bioconda patch
Add container mulled-v2-d75ec9974c9e3c2926225cf4fda917e64a9a821f:8a3f298eb1a2bc5c90055debf133e2c72e21b8c0
…344769cb3a7383b2da4aa6c4cf6e510303e0. **Hash**: mulled-v2-63feb106b58570bb035d9cc78b5ae437b57ee23d:7320344769cb3a7383b2da4aa6c4cf6e510303e0 **Packages**: - lexicmap=0.8.0 - file=5.46 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - lexicmap-index.xml - lexicmap.xml Generated with Planemo.
…4c9e658f3086fb31ddf84fb7a4525cb61e2d. **Hash**: mulled-v2-c742dccc9d8fabfcff2af0d8d6799dbc711366cf:3ce44c9e658f3086fb31ddf84fb7a4525cb61e2d **Packages**: - bowtie2=2.5.4 - samtools=1.22.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - bowtie2_wrapper.xml Generated with Planemo.
…adc2e590f0505d22bb16d66a27284a0a5591. **Hash**: mulled-v2-a1e116d3536834ecbbada3c89e7eb04341cbc496:e84fadc2e590f0505d22bb16d66a27284a0a5591 **Packages**: - r-ggrepel=0.9.6 - r-ggplot2=4.0.0 - r-dplyr=1.1.4 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - volcanoplot.xml Generated with Planemo.
…f21e8a1a985bf6e29f00c68c4b2e33663529. **Hash**: mulled-v2-31457b56c9a9c57b2aa348290faca1623bd406a7:e912f21e8a1a985bf6e29f00c68c4b2e33663529 **Packages**: - cutesv=2.1.3 - samtools=1.22.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - cutesv.xml Generated with Planemo.
…d6e4af5b514ba927fb9ab600e8d52645fd12. **Hash**: mulled-v2-d3567f5619929c65634ae5e58d309a2d5e1103f3:1749d6e4af5b514ba927fb9ab600e8d52645fd12 **Packages**: - perl-math-cdf=0.1 - ensembl-vep=115.2 - grep=3.11 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - ensembl_vep.xml Generated with Planemo.
…ccb94660362887b3fc4789adf9dd3b3f1671. **Hash**: mulled-v2-e15f4d05b9fb9094efa8549db09ec3c886f8a552:fda4ccb94660362887b3fc4789adf9dd3b3f1671 **Packages**: - rrmscorer=1.0.11 - seaborn-base=0.11.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - RRMScorer.xml Generated with Planemo.
**Hash**: rp2paths:2.0.0 **Packages**: - rp2paths=2.0.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - rp2paths.xml Generated with Planemo.
…8fabfcff2af0d8d6799dbc711366cf-3ce44c9e658f3086fb31ddf84fb7a4525cb61e2d Add container mulled-v2-c742dccc9d8fabfcff2af0d8d6799dbc711366cf:3ce44c9e658f3086fb31ddf84fb7a4525cb61e2d.
Add container rp2paths:2.0.0.
…fb9094efa8549db09ec3c886f8a552-fda4ccb94660362887b3fc4789adf9dd3b3f1671 Add container mulled-v2-e15f4d05b9fb9094efa8549db09ec3c886f8a552:fda4ccb94660362887b3fc4789adf9dd3b3f1671.
…929c65634ae5e58d309a2d5e1103f3-1749d6e4af5b514ba927fb9ab600e8d52645fd12 Add container mulled-v2-d3567f5619929c65634ae5e58d309a2d5e1103f3:1749d6e4af5b514ba927fb9ab600e8d52645fd12.
…a9c57b2aa348290faca1623bd406a7-e912f21e8a1a985bf6e29f00c68c4b2e33663529 Add container mulled-v2-31457b56c9a9c57b2aa348290faca1623bd406a7:e912f21e8a1a985bf6e29f00c68c4b2e33663529.
…6834ecbbada3c89e7eb04341cbc496-e84fadc2e590f0505d22bb16d66a27284a0a5591 Add container mulled-v2-a1e116d3536834ecbbada3c89e7eb04341cbc496:e84fadc2e590f0505d22bb16d66a27284a0a5591.
**Hash**: galaxy-util:25.1 **Packages**: - galaxy-util=25.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - archive_to_directory.xml Generated with Planemo.
Add container galaxy-util:25.1.
**Hash**: galaxy-util:25.0.2 **Packages**: - galaxy-util=25.0.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - joiner.xml Generated with Planemo.
…54cd8bd150dbd2e4456f4738abba19aae8b3. **Hash**: mulled-v2-5ab22bce50c3ef06dcba7de769e6366ad3df6250:2d3e54cd8bd150dbd2e4456f4738abba19aae8b3 **Packages**: - parallel=20250822 - snp-pileup=0.6.2 - htslib=1.22.1 - samtools=1.22.1 - bcftools=1.22 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - snp_pileup_for_facets.xml Generated with Planemo.
…42436a8b5539422faeeae4ff0c81e1e4e200. **Hash**: mulled-v2-cafc589522afd600e06b8bbf6d88159aa82337be:860b42436a8b5539422faeeae4ff0c81e1e4e200 **Packages**: - jbrowse2=3.6.5 - tabix=1.11 - python=3.13.7 - requests=2.32.5 - samtools=1.22.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - jbrowse2.xml Generated with Planemo.
…aa4919ee282a4213ea98fe054dc9afddff0d. **Hash**: mulled-v2-9ac7656556977f8f34d5c370be727508e3216354:3306aa4919ee282a4213ea98fe054dc9afddff0d **Packages**: - numpy=2.3.5 - ome-zarr=0.12.2 - tifffile=2025.10.16 - scipy=1.16.3 - giatools=0.6.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - filter.xml Generated with Planemo.
…977f8f34d5c370be727508e3216354-3306aa4919ee282a4213ea98fe054dc9afddff0d Add container mulled-v2-9ac7656556977f8f34d5c370be727508e3216354:3306aa4919ee282a4213ea98fe054dc9afddff0d.
…c9135c70ae4cb6630e85624c2c4d60449a96. **Hash**: mulled-v2-b8c00919e78e310f5965a5971fdc4280dbc6cc1c:a785c9135c70ae4cb6630e85624c2c4d60449a96 **Packages**: - ca-certificates=2025.8.3 - ncbi-datasets-cli=18.13.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - datasets_gene.xml - datasets_genome.xml Generated with Planemo.
…8e310f5965a5971fdc4280dbc6cc1c-a785c9135c70ae4cb6630e85624c2c4d60449a96 Add container mulled-v2-b8c00919e78e310f5965a5971fdc4280dbc6cc1c:a785c9135c70ae4cb6630e85624c2c4d60449a96.
Update hash.tsv
…84cee42c223eac2c22e6601155b3dfd63f21. **Hash**: mulled-v2-8dced595a852b857884a7051efc56ae9182c3b26:76f684cee42c223eac2c22e6601155b3dfd63f21 **Packages**: - giatools=0.5.2 - pyyaml=6.0.3 - highdicom=0.27.0 - pydicom=3.0.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - dicom2tiff.xml - dicom2text.xml Generated with Planemo.
…52b857884a7051efc56ae9182c3b26-76f684cee42c223eac2c22e6601155b3dfd63f21 Add container mulled-v2-8dced595a852b857884a7051efc56ae9182c3b26:76f684cee42c223eac2c22e6601155b3dfd63f21.
…f870bedadfd56454e642b719ac19184cb7ed. **Hash**: mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed **Packages**: - giatools=0.7.3 - scikit-image=0.25.2 - ome-zarr=0.12.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - auto_threshold.xml Generated with Planemo.
…71a0502a1d0be36e13d3b627430d47349af0. **Hash**: mulled-v2-5e9947bf5c19a0756bd8fa6f3ff73588cdf1ae72:90e971a0502a1d0be36e13d3b627430d47349af0 **Packages**: - scipy=1.16.3 - giatools=0.7.3 - ome-zarr=0.12.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - binary2label.xml Generated with Planemo.
…975be3b1acef6baca5fb04a3b3834cba60a3. **Hash**: mulled-v2-29a5f6e2e787077bbfba4cca3bd6440bcf74a622:f018975be3b1acef6baca5fb04a3b3834cba60a3 **Packages**: - pandas=2.2.2 - giatools=0.7.3 - scikit-image=0.25.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - 2d_filter_segmentation_by_features.xml Generated with Planemo.
…19a0756bd8fa6f3ff73588cdf1ae72-90e971a0502a1d0be36e13d3b627430d47349af0 Add container mulled-v2-5e9947bf5c19a0756bd8fa6f3ff73588cdf1ae72:90e971a0502a1d0be36e13d3b627430d47349af0.
…73445b115df8bb46e40eaa3d54b806-33baf870bedadfd56454e642b719ac19184cb7ed Add container mulled-v2-73e393604573445b115df8bb46e40eaa3d54b806:33baf870bedadfd56454e642b719ac19184cb7ed.
…87077bbfba4cca3bd6440bcf74a622-f018975be3b1acef6baca5fb04a3b3834cba60a3 Add container mulled-v2-29a5f6e2e787077bbfba4cca3bd6440bcf74a622:f018975be3b1acef6baca5fb04a3b3834cba60a3.
Add base image for `libcarna-python=0.2.0`
…b55c65ab800f9ea9f51426d028e465201b0e. **Hash**: mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e **Packages**: - scikit-image=0.25.2 - pandas=2.2.2 - giatools=0.7.3 - ome-zarr=0.12.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - 2d_feature_extraction.xml Generated with Planemo.
…c576b8398d00911c4ecec5c3fb8ecf52380d. **Hash**: mulled-v2-4e3baf4339bbc9ba7ac9b60fb3e9dc0fe01fd085:e88ac576b8398d00911c4ecec5c3fb8ecf52380d **Packages**: - giatools=0.7.3 - ome-zarr=0.12.2 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - clip_image.xml Generated with Planemo.
…ba55718d4d83b71ccc43a5b16aa8e6-b4d5b55c65ab800f9ea9f51426d028e465201b0e Add container mulled-v2-2ae8cd6803ba55718d4d83b71ccc43a5b16aa8e6:b4d5b55c65ab800f9ea9f51426d028e465201b0e.
…bbc9ba7ac9b60fb3e9dc0fe01fd085-e88ac576b8398d00911c4ecec5c3fb8ecf52380d Add container mulled-v2-4e3baf4339bbc9ba7ac9b60fb3e9dc0fe01fd085:e88ac576b8398d00911c4ecec5c3fb8ecf52380d.
**Hash**: cellpose:4.0.8 **Packages**: - cellpose=4.0.8 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - cellpose.xml Generated with Planemo.
…80b6084ff8bdd6b26346c95747fbfe6a9a06. **Hash**: mulled-v2-5f5572acbb4778dc6a42fdb81d01e74c962d7fde:691f80b6084ff8bdd6b26346c95747fbfe6a9a06 **Packages**: - python=3.13 - openai=2.7.1 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - chatgpt.xml Generated with Planemo.
…4778dc6a42fdb81d01e74c962d7fde-691f80b6084ff8bdd6b26346c95747fbfe6a9a06 Add container mulled-v2-5f5572acbb4778dc6a42fdb81d01e74c962d7fde:691f80b6084ff8bdd6b26346c95747fbfe6a9a06.
Add container cellpose:4.0.8.
…f11b1c5f43a371b9373217d6b5ce8a77c610. **Hash**: mulled-v2-b8c00919e78e310f5965a5971fdc4280dbc6cc1c:9dbaf11b1c5f43a371b9373217d6b5ce8a77c610 **Packages**: - ncbi-datasets-cli=18.14.0 - ca-certificates=2026.1.4 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - datasets_gene.xml - datasets_genome.xml Generated with Planemo.
…8e310f5965a5971fdc4280dbc6cc1c-9dbaf11b1c5f43a371b9373217d6b5ce8a77c610 Add container mulled-v2-b8c00919e78e310f5965a5971fdc4280dbc6cc1c:9dbaf11b1c5f43a371b9373217d6b5ce8a77c610.
…c79fc5cf1d349a1a185b0f0680156e9a0833. **Hash**: mulled-v2-c02993c9a31c10b5a2baf113eacd027e8253bffa:0a4ec79fc5cf1d349a1a185b0f0680156e9a0833 **Packages**: - tesseract=5.5.2 - poppler=25.07.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - tesseract.xml Generated with Planemo.
…1c10b5a2baf113eacd027e8253bffa-0a4ec79fc5cf1d349a1a185b0f0680156e9a0833 Add container mulled-v2-c02993c9a31c10b5a2baf113eacd027e8253bffa:0a4ec79fc5cf1d349a1a185b0f0680156e9a0833.
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