Merge branch 'master' into mulled-v2-3b8ae3f63a29f67694ef6c56735fdbc8b6519912-842e75e30f6994b31f15767c30292769e5207fab

bgruening · web-flow · commit 068116023994 · 2025-12-10T08:35:28.000+01:00
diff --git a/combinations/galaxy_sequence_utils:1.2-0.tsv b/combinations/galaxy_sequence_utils:1.2-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+galaxy_sequence_utils=1.2	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/hash.tsv b/combinations/hash.tsv
@@ -928,3 +928,4 @@ bioconductor-resolve=1.8.0,bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.5,r-patc
 gawk=5.0.1,snpeff=5.2	quay.io/bioconda/base-glibc-busybox-bash:latest	2
 r-base=4.3.3,bioconductor-rtracklayer=1.62.0,r-optparse=1.7.4,r-dplyr=1.1.4,r-stringr=1.5.1,r-plyr=1.8.9,r-data.table=1.15.2,coreutils=9.5,r-argparse=2.2.2,r-tidyverse=2.0.0
 unzip=6.0,tar=1.34,findutils=4.10.0
+bwa=0.7.19,samtools=1.22
diff --git a/combinations/metawrap-binning:1.3.0-0.tsv b/combinations/metawrap-binning:1.3.0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+metawrap-binning=1.3.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-00d89f270f9a6abe582ea952862b5d6108ec1636:390ed32e980fdf85eca7bfbf9c142855d0b55fba-0.tsv b/combinations/mulled-v2-00d89f270f9a6abe582ea952862b5d6108ec1636:390ed32e980fdf85eca7bfbf9c142855d0b55fba-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+goalign=0.3.9,gotree=0.5.0,phyml=3.3.20190909	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-02a41624d4a53bf3251489da44351a744df3d0e6:e4d4a0610abb88ec7d5e2db2162c60a0f1da8344-0.tsv b/combinations/mulled-v2-02a41624d4a53bf3251489da44351a744df3d0e6:e4d4a0610abb88ec7d5e2db2162c60a0f1da8344-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+mafft=7.525,ruby=3.4.5	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-06cd3f248c1be5bdd2a673d7c327c834d03bcc0b:2e3f4573ce0063b90d8699a28378c05522e346e4-0.tsv b/combinations/mulled-v2-06cd3f248c1be5bdd2a673d7c327c834d03bcc0b:2e3f4573ce0063b90d8699a28378c05522e346e4-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+bmge=1.12,goalign=0.3.9	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-077b852b8b5440d395ad23f9f24f50c943390a84:637752cee5173d8537729a93c5aa9ea3a70f45bb-0.tsv b/combinations/mulled-v2-077b852b8b5440d395ad23f9f24f50c943390a84:637752cee5173d8537729a93c5aa9ea3a70f45bb-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+ucsc-bigwigtobedgraph=377,pretextgraph=0.0.9	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-0ce81b0672b34c2cb41c8710f4b31136f1a9fa46:7794855e31b53df81ea6a18cf34d8f807158ce75-0.tsv b/combinations/mulled-v2-0ce81b0672b34c2cb41c8710f4b31136f1a9fa46:7794855e31b53df81ea6a18cf34d8f807158ce75-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+gzip=1.14,mosdepth=0.3.12	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-1969271ffece8920441ded0a2410f8218b13d934:26927cc8a3379b9b4a7238e31d2f87e9a49a48d0-0.tsv b/combinations/mulled-v2-1969271ffece8920441ded0a2410f8218b13d934:26927cc8a3379b9b4a7238e31d2f87e9a49a48d0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+giatools=0.3.1,numpy=2.3.4,pandas=2.3.3,scikit-image=0.25.2,tifffile=2025.10.16	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-1bd7c143fec0659638fb990d05ec2cc030bd8b61:aa256f71b8d4dbbeccb3f680be785adb051f499c-0.tsv b/combinations/mulled-v2-1bd7c143fec0659638fb990d05ec2cc030bd8b61:aa256f71b8d4dbbeccb3f680be785adb051f499c-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+coreprofiler=1.1.7,blast=2.16.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-2d89def15ec5f0c75249c2ee4ca452038958f94e:2f43fa471a1926ce923a7fe01d7303b05a025fc1-0.tsv b/combinations/mulled-v2-2d89def15ec5f0c75249c2ee4ca452038958f94e:2f43fa471a1926ce923a7fe01d7303b05a025fc1-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+pandas=2.3.3,python=3.11.14,ncbi-amrfinderplus=4.0.23	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-2f6e435d4aa1a5abd2820be7bad83f4724be5ce9:c035b96ccef2f7fcdb94eb4259dcd1ddd095eb68-0.tsv b/combinations/mulled-v2-2f6e435d4aa1a5abd2820be7bad83f4724be5ce9:c035b96ccef2f7fcdb94eb4259dcd1ddd095eb68-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+goalign=0.3.9,mrbayes=3.2.7,gotree=0.5.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-433a4f3759462347eb497ad0b95240673a0c4fc6:b1047217de86a4dc6041c006a37c6ed84aa3c946-0.tsv b/combinations/mulled-v2-433a4f3759462347eb497ad0b95240673a0c4fc6:b1047217de86a4dc6041c006a37c6ed84aa3c946-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+seqtk=1.4,metaphlan=4.2.4	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-47f8c4dccbd92dd50139c3b19f499a6da1e387d8:f6082996f2a3a5265ebb1014887e638a27b8ebed-0.tsv b/combinations/mulled-v2-47f8c4dccbd92dd50139c3b19f499a6da1e387d8:f6082996f2a3a5265ebb1014887e638a27b8ebed-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+fgbio=2.1.0,samtools=1.22	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-9e8e33438a9f45baa22f5d2a77c3b06de32a5c1e:959ba8b0e90fcb2a734e53c96b697ed530c289d6-0.tsv b/combinations/mulled-v2-9e8e33438a9f45baa22f5d2a77c3b06de32a5c1e:959ba8b0e90fcb2a734e53c96b697ed530c289d6-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+python=2.7,aragorn=1.2.41	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-a1e116d3536834ecbbada3c89e7eb04341cbc496:25bcdd19adfdb29abfb40c3546cb87a2cff76ed4-0.tsv b/combinations/mulled-v2-a1e116d3536834ecbbada3c89e7eb04341cbc496:25bcdd19adfdb29abfb40c3546cb87a2cff76ed4-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+r-ggplot2=4.0.1,r-ggrepel=0.9.6,r-dplyr=1.1.4	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:fdf1f306906e1636d3780e0df97d8d8dc7656c61-0.tsv b/combinations/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:fdf1f306906e1636d3780e0df97d8d8dc7656c61-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+tar=1.34,pigz=2.8,meryl=1.4.1,merqury=1.1	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-ba8b9a5fddba18cb2c9b99343877e257db6e5339:8e317420032f26ab5ca5c4208ef13cab94bf9c20-0.tsv b/combinations/mulled-v2-ba8b9a5fddba18cb2c9b99343877e257db6e5339:8e317420032f26ab5ca5c4208ef13cab94bf9c20-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+goalign=0.3.9,gotree=0.5.0,fastme=2.1.6.3	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-c02993c9a31c10b5a2baf113eacd027e8253bffa:02a545ce215d1da8234d92234381f435552f0578-0.tsv b/combinations/mulled-v2-c02993c9a31c10b5a2baf113eacd027e8253bffa:02a545ce215d1da8234d92234381f435552f0578-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+tesseract=5.5.1,poppler=25.07.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-cafc589522afd600e06b8bbf6d88159aa82337be:1dacc45f7ed5821c2620ba915719ca19a2a7ce13-0.tsv b/combinations/mulled-v2-cafc589522afd600e06b8bbf6d88159aa82337be:1dacc45f7ed5821c2620ba915719ca19a2a7ce13-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+tabix=1.11,jbrowse2=3.7.0,python=3.13.7,samtools=1.22.1,requests=2.32.5	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-dd29a726a518ab18d2113433052947ad2389bdcd:d6700a62b018c849d5264f20fbcc0f80b94ba259-0.tsv b/combinations/mulled-v2-dd29a726a518ab18d2113433052947ad2389bdcd:d6700a62b018c849d5264f20fbcc0f80b94ba259-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+csvtk=0.35.0,pangolin=4.3.4,gofasta=1.2.3,pangolin-data=1.36,scorpio=0.3.19,ucsc-fatovcf=482,grep=3.12,constellations=0.1.12,minimap2=2.30,usher=0.6.6	quay.io/bioconda/base-glibc-debian-bash:latest	0
diff --git a/combinations/mulled-v2-f01f06279bda3ab7b984d20f581e41b1a4741c67:3bd9d38ad5f1571f459ebe1c3adfd99947f267c2-0.tsv b/combinations/mulled-v2-f01f06279bda3ab7b984d20f581e41b1a4741c67:3bd9d38ad5f1571f459ebe1c3adfd99947f267c2-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+snapatac2=2.8.0,polars=1.31.0,umap-learn=0.5.7,harmonypy=0.0.10,python-kaleido=0.2.1,plotly=5.24.1,xgboost=3.0.4,scanorama=1.7.4,leidenalg=0.10.2,hdbscan=0.8.37	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-f0ccafb75d03ceda999d774f01435b6117d5a6db:fe6381a1fd7fec7ff19c8d467e6e029135812a10-0.tsv b/combinations/mulled-v2-f0ccafb75d03ceda999d774f01435b6117d5a6db:fe6381a1fd7fec7ff19c8d467e6e029135812a10-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+gblocks=0.91b,goalign=0.3.9	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-f2c828284650a993a9ae95ad0886a156bed411a0:a03a5235f88ae98e4a6f2c35df038f332825a988-0.tsv b/combinations/mulled-v2-f2c828284650a993a9ae95ad0886a156bed411a0:a03a5235f88ae98e4a6f2c35df038f332825a988-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+unzip=6.0,wget=1.25.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/mulled-v2-fdcde7f8b012dd5952a929882e18729b4dc795ff:2b7677c1ef610ec66b30535e6d29cbb2f01ed2ac-0.tsv b/combinations/mulled-v2-fdcde7f8b012dd5952a929882e18729b4dc795ff:2b7677c1ef610ec66b30535e6d29cbb2f01ed2ac-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+fasttree=2.1.11,goalign=0.3.9,gotree=0.5.0,parallel=20250622	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/python:3.12.12-0.tsv b/combinations/python:3.12.12-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+python=3.12.12	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/rp2paths:2.1.3-0.tsv b/combinations/rp2paths:2.1.3-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+rp2paths=2.1.3	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/rp2paths:2.1.4-0.tsv b/combinations/rp2paths:2.1.4-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+rp2paths=2.1.4	quay.io/bioconda/base-glibc-busybox-bash:latest	0

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+galaxy_sequence_utils=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+metawrap-binning=1.3.0 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+goalign=0.3.9,gotree=0.5.0,phyml=3.3.20190909 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+mafft=7.525,ruby=3.4.5 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+bmge=1.12,goalign=0.3.9 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+ucsc-bigwigtobedgraph=377,pretextgraph=0.0.9 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+gzip=1.14,mosdepth=0.3.12 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+giatools=0.3.1,numpy=2.3.4,pandas=2.3.3,scikit-image=0.25.2,tifffile=2025.10.16 quay.io/bioconda/base-glibc-busybox-bash:latest 0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+#targets base_image image_build`
	`2`	`+coreprofiler=1.1.7,blast=2.16.0 quay.io/bioconda/base-glibc-busybox-bash:latest 0`