Updated trusted tools (2024-03-02)

Bio2Byte · Mar 2, 2024 · 2b09e82 · 2b09e82
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diff --git a/climate.yaml.lock b/climate.yaml.lock
@@ -242,6 +242,7 @@ tools:
 - name: ggplot2_heatmap2
   owner: iuc
   revisions:
+  - 374e9062d874
   - 53460afd5115
   - '566197475670'
   - ca7cb0eaad62

diff --git a/ecology.yaml.lock b/ecology.yaml.lock
@@ -206,6 +206,7 @@ tools:
   owner: bgruening
   revisions:
   - 0a8c6b61f0f4
+  - 12615d397df7
   - d698c222f354
   - ddf54b12c295
   - f46f0e4f75c4
@@ -532,6 +533,7 @@ tools:
 - name: ggplot2_heatmap2
   owner: iuc
   revisions:
+  - 374e9062d874
   - 53460afd5115
   - '566197475670'
   - ca7cb0eaad62

diff --git a/genome-annotation.yaml.lock b/genome-annotation.yaml.lock
@@ -248,6 +248,7 @@ tools:
   owner: genouest
   revisions:
   - 7bc75dd0f782
+  - 7c1dc010a819
   tool_panel_section_label: Annotation
 - name: manta
   owner: artbio

diff --git a/goeckslab.yaml.lock b/goeckslab.yaml.lock
@@ -6,32 +6,38 @@ tools:
   owner: goeckslab
   revisions:
   - 6df8d6e42152
+  - 8097f9124f87
   tool_panel_section_label: Imaging
 - name: vitessce_spatial
   owner: goeckslab
   revisions:
+  - 4bf852448b5d
   - 9f60ef2d586e
   tool_panel_section_label: Imaging
 - name: mesmer
   owner: goeckslab
   revisions:
   - 02abff468d60
   - 187918c47051
+  - 2675ff99a53b
   - 53240d7c1fc5
   - c60b810d570d
   tool_panel_section_label: Spatial Omics
 - name: squidpy
   owner: goeckslab
   revisions:
+  - bad34051dc8a
   - be0e7952e229
   tool_panel_section_label: Imaging
 - name: rename_tiff_channels
   owner: goeckslab
   revisions:
   - 09e240a12897
+  - d2c59a1ac0c4
   tool_panel_section_label: Imaging
 - name: cell_intensity_processing
   owner: goeckslab
   revisions:
   - 7a77ed0e579a
+  - 7f93f472a242
   tool_panel_section_label: Imaging
diff --git a/imaging.yaml.lock b/imaging.yaml.lock
@@ -547,6 +547,7 @@ tools:
 - name: bioformats2raw
   owner: imgteam
   revisions:
+  - 1b3e7d53cec6
   - 4b6c2135e547
   - b32f5368e279
   tool_panel_section_label: Imaging

diff --git a/single-cell-ebi-gxa.yaml.lock b/single-cell-ebi-gxa.yaml.lock
@@ -95,6 +95,7 @@ tools:
   - 98f37271c17c
   - a0274bc43b7e
   - a36d7a315be7
+  - a4774b7b2e85
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   - c09d61ede252
   - d868221262d5
@@ -109,6 +110,7 @@ tools:
   - 087a7edb0995
   - 0fe56ddbab0d
   - 1dc0ea7a7e62
+  - 22bd5861706d
   - 232937b5bb8f
   - 2401808e20e8
   - 3bce5710a90b
@@ -149,6 +151,7 @@ tools:
   - 9f0ca1641ab2
   - b28ba58033ea
   - ba64b91ed2b9
+  - bf1e0bdec1db
   - c23d0ff783d4
   - da8c130348b6
   - dcfb23758646
@@ -175,6 +178,7 @@ tools:
   - 9a36525a8425
   - a1698b43abeb
   - c678f671e151
+  - cc64914b0cf4
   - d1b97a5d5a8d
   - d82d999fa716
   - da2808112bb4
@@ -191,6 +195,7 @@ tools:
   - 2784759ad631
   - 2ccd9f9e2cd0
   - 35caf3c27c91
+  - 36735850e461
   - 455846afcc73
   - 5a62843a2b9f
   - 5e68e130fafe
@@ -234,6 +239,7 @@ tools:
   - c18f446dcfbf
   - c608fd80ec15
   - cc776860fae1
+  - d8f5224005bb
   - eb01a7e59e9a
   - f00adc96e0bf
   - f04dd4e5b6a7
@@ -249,6 +255,7 @@ tools:
   - 258e13397a8a
   - 273faaa2bd69
   - 2861ca3bfe4d
+  - 2bc42a6f092b
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   - 321f1b073cbc
   - 438a09194001
@@ -274,6 +281,7 @@ tools:
   - 1dda36e73482
   - 28ab1cdd0cf5
   - 28b1546857b0
+  - 3027cb62adbd
   - 3636ec97f3af
   - 3a4564b9d685
   - 439f7f939d46
@@ -300,6 +308,7 @@ tools:
   - 40feaaed47cf
   - 4bb2ca8e2bd3
   - 645f12f44a6d
+  - 73d43034c860
   - 7c4d44c14ceb
   - 81069608d570
   - 93680e2ff8f4
@@ -329,6 +338,7 @@ tools:
   - 56d22aa6cb3b
   - 68e82882a8f9
   - 7c601934578b
+  - 7d5c97823f8b
   - 882f4671d686
   - 99dd7baf9e23
   - 9fafbfcdee0d
@@ -356,6 +366,7 @@ tools:
   - 8e2fc37c3e0c
   - 9d746af31fe8
   - c99f397434a3
+  - cb1992d1804b
   - d3df472a21dc
   - d8423c3f869d
   - e8e54d565c92
@@ -365,6 +376,7 @@ tools:
 - name: scanpy_read_10x
   owner: ebi-gxa
   revisions:
+  - 078aa23c9374
   - 1b84ae7595ed
   - 247e401d454f
   - 287503c35cb4
@@ -390,6 +402,7 @@ tools:
 - name: scanpy_regress_variable
   owner: ebi-gxa
   revisions:
+  - 0bab2ae44e7a
   - 1200b55768ce
   - 1ad1d9713563
   - 2131ec9d52e2
@@ -421,6 +434,7 @@ tools:
   - 6a6364b488db
   - 713e94af9d6c
   - 722ba62d7bb4
+  - 79cc06a557b0
   - 7abe27a3866e
   - 83baf6001a10
   - 8e45c89adab2
@@ -435,6 +449,7 @@ tools:
 - name: scanpy_run_dpt
   owner: ebi-gxa
   revisions:
+  - 03921aa8b29c
   - 0e264c40fd06
   - 12f67b0c1a94
   - 1ab80fc6f667
@@ -474,6 +489,7 @@ tools:
   - 932e99b4dc5f
   - a6190ae4fe16
   - a82c905e2c26
+  - be019b069e31
   - cef0ddd01875
   - d929261bc28c
   - f5bc7d1b32fd
@@ -491,6 +507,7 @@ tools:
   - 9dcd0b02d686
   - a12f0d1b0fac
   - a9e541954c1c
+  - b2768cae00a1
   - b9ccaa957667
   - d811772b94d7
   - eba43c4d86b9
@@ -508,6 +525,7 @@ tools:
   - 1618435e2a33
   - 2dd53b944e78
   - 3ee74b58c72d
+  - 4428dba93375
   - 4a54b92af339
   - 4fbc4b97090f
   - 5063cd7f8c89
@@ -543,6 +561,7 @@ tools:
   - 8eff7ec034e3
   - 9d2b6c6f9e07
   - a597590ccf6c
+  - abdb61e4afa3
   - af9b447bcde8
   - b5e1939cc155
   - b946c0c60d4c
@@ -576,6 +595,7 @@ tools:
   - bd4a244faeb8
   - c111d7d04f0b
   - e31937baa330
+  - ea91cfd0444e
   - fe562424a0a6
   tool_panel_section_id: hca_sc_scanpy_tools
 - name: scanpy_scale_data
@@ -587,6 +607,7 @@ tools:
   - 33d809001520
   - 3a0d4bebabc5
   - 4c73b070cbff
+  - 4cc9362782b4
   - 4f04a735b26d
   - 5605f8452eb3
   - 796cd21bb304
@@ -612,6 +633,7 @@ tools:
   - 2de673ef8c13
   - 352cdf3b2f75
   - 3c2ff50cef4a
+  - 3c47bc560688
   - 5c25b8a985e8
   - 7322e7583847
   - 7a573108f5f4
@@ -630,6 +652,7 @@ tools:
   - 6903bc865d63
   - 739f68e3cbca
   - bf824765919c
+  - c354af93f567
   - c8eb5547846b
   - ca0c7251e415
   tool_panel_section_id: hca_sc_scanpy_tools
@@ -647,6 +670,7 @@ tools:
   - dc7fa97154f1
   - e9788746e0f6
   - eb30e34367b1
+  - ff6decc0f432
   tool_panel_section_id: hca_sc_scanpy_tools
 - name: scanpy_integrate_bbknn
   owner: ebi-gxa
@@ -661,6 +685,7 @@ tools:
   - 89eef46fce58
   - 932f0f51074c
   - 9d76c3d6dff6
+  - c9da9192eee5
   - de8643b6e419
   tool_panel_section_id: hca_sc_scanpy_tools
 - name: scanpy_plot_scrublet
@@ -669,10 +694,12 @@ tools:
   - 021a6e341dcf
   - 2d3b13bb704a
   - 4276a6dea8d1
+  - 6f5509cf3176
   tool_panel_section_id: hca_sc_scanpy_tools
 - name: scanpy_multiplet_scrublet
   owner: ebi-gxa
   revisions:
+  - 2f9517a24c73
   - 8ca3ab8300ce
   - b8126b3bf5d0
   - fadc4fbf8025
@@ -690,6 +717,7 @@ tools:
   - 89eef46fce58
   - 932f0f51074c
   - 9d76c3d6dff6
+  - c9da9192eee5
   - de8643b6e419
   tool_panel_section_id: hca_sc_scanpy_tools
 - name: seurat_create_seurat_object
@@ -701,6 +729,7 @@ tools:
   owner: ebi-gxa
   revisions:
   - 316623eb59bd
+  - 64174ac50d78
   - 6e26ee99fdfc
   - cfc3d8ee3a64
   - daeca8f7a26e
@@ -710,6 +739,7 @@ tools:
   owner: ebi-gxa
   revisions:
   - 249392cd0d99
+  - 36221da750e8
   - 80eec773c961
   - 8c2b1d2659df
   - a18f8d34524a
@@ -722,6 +752,7 @@ tools:
   - 3c41916bc2ad
   - c1848daebad1
   - c4b984347138
+  - cd9f564bd63f
   - ebf7286c8b97
   tool_panel_section_id: hca_sc_seurat_tools
 - name: seurat_find_clusters
@@ -731,11 +762,13 @@ tools:
   - 8ea738667314
   - 8ed848ef86fd
   - bdabb6af06e4
+  - d541e9e62beb
   - eefaffdcd441
   tool_panel_section_id: hca_sc_seurat_tools
 - name: seurat_find_markers
   owner: ebi-gxa
   revisions:
+  - 07fc9f4841b3
   - 203dcb6f2faf
   - 3dd20b758756
   - 7895b4bb6247
@@ -748,12 +781,14 @@ tools:
   - 051953328516
   - 5a79dc04aafe
   - 5be60722113a
+  - 948fc0276b4f
   - a56efad05337
   - a6077346f869
   tool_panel_section_id: hca_sc_seurat_tools
 - name: seurat_normalise_data
   owner: ebi-gxa
   revisions:
+  - 3f49bc9c9213
   - 48174ec556de
   - 619fead82856
   - 778e1a98055f
@@ -768,11 +803,13 @@ tools:
   - 301cf1b4b43d
   - 893ea1e1eed3
   - 948ce48561f9
+  - f5db0e853f57
   tool_panel_section_id: hca_sc_seurat_tools
 - name: seurat_run_pca
   owner: ebi-gxa
   revisions:
   - 3fd59cdcb477
+  - 8ded486b0014
   - 9547ebb03f6f
   - a54f3400a885
   - c4607a42113e
@@ -782,6 +819,7 @@ tools:
   owner: ebi-gxa
   revisions:
   - 050fe6894b74
+  - 0db997e4a81d
   - 13a27436f8ee
   - 2d294978b152
   - 3aea769deab1
@@ -793,6 +831,7 @@ tools:
   - 1656179f8e7c
   - 3d0bfc2a233e
   - 4147dc085d45
+  - 5e9ba303f9e1
   - 6166efaeb4a6
   - d2f6eac0ad42
   tool_panel_section_id: hca_sc_seurat_tools
@@ -803,6 +842,7 @@ tools:
   - 4fff8ad1c76d
   - 99d628557c47
   - ab622ffd7c7f
+  - ba897c57bdd9
   tool_panel_section_id: hca_sc_seurat_tools
 - name: monocle3_create
   owner: ebi-gxa
@@ -1003,6 +1043,7 @@ tools:
   owner: bgruening
   revisions:
   - 0a8c6b61f0f4
+  - 12615d397df7
   - 9ff72e942410
   - d698c222f354
   - ddf54b12c295