Skip to content

Commit d68d15b

Browse files
author
planemo-autoupdate
committed
Updating workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation from 1.0beta6 to 1.0b7
1 parent 9d5c3c4 commit d68d15b

File tree

2 files changed

+98
-43
lines changed

2 files changed

+98
-43
lines changed

workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,13 @@
11
# Changelog
22

3+
## [1.0b7] - 2025-07-14
4+
5+
### Automatic update
6+
- `toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0`
7+
- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0`
8+
- `toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.5+galaxy0`
9+
- `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0`
10+
311
## [1.0beta6] - 2025-06-09
412

513
### Changes

workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga

Lines changed: 90 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -177,7 +177,6 @@
177177
],
178178
"format-version": "0.1",
179179
"license": "MIT",
180-
"release": "1.0beta6",
181180
"name": "PretextMap Generation from 1 or 2 haplotypes",
182181
"report": {
183182
"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -533,7 +532,12 @@
533532
"output_name": "output"
534533
}
535534
},
536-
"inputs": [],
535+
"inputs": [
536+
{
537+
"description": "runtime parameter for tool Map parameter value",
538+
"name": "input_param_type"
539+
}
540+
],
537541
"label": "Hap2 not provided",
538542
"name": "Map parameter value",
539543
"outputs": [
@@ -1113,7 +1117,7 @@
11131117
}
11141118
},
11151119
"tags": [],
1116-
"uuid": "8fb65374-0776-4aa9-80d8-eb0b8c69f274"
1120+
"uuid": "4f7fc643-417e-4016-a589-caa54db2f004"
11171121
},
11181122
"tool_id": null,
11191123
"type": "subworkflow",
@@ -1458,7 +1462,7 @@
14581462
}
14591463
},
14601464
"tags": [],
1461-
"uuid": "c32e34b2-4390-4bf2-9048-411280d63ddd"
1465+
"uuid": "3c816783-2f45-46f1-b97c-e92df597510e"
14621466
},
14631467
"tool_id": null,
14641468
"type": "subworkflow",
@@ -1694,7 +1698,12 @@
16941698
"output_name": "output"
16951699
}
16961700
},
1697-
"inputs": [],
1701+
"inputs": [
1702+
{
1703+
"description": "runtime parameter for tool Cutadapt",
1704+
"name": "library"
1705+
}
1706+
],
16981707
"label": "Trim Hi-C reads 2",
16991708
"name": "Cutadapt",
17001709
"outputs": [
@@ -1819,7 +1828,7 @@
18191828
},
18201829
"5": {
18211830
"annotation": "",
1822-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4",
1831+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0",
18231832
"errors": null,
18241833
"id": 5,
18251834
"input_connections": {
@@ -1832,7 +1841,16 @@
18321841
"output_name": "output"
18331842
}
18341843
},
1835-
"inputs": [],
1844+
"inputs": [
1845+
{
1846+
"description": "runtime parameter for tool BWA-MEM2",
1847+
"name": "fastq_input"
1848+
},
1849+
{
1850+
"description": "runtime parameter for tool BWA-MEM2",
1851+
"name": "reference_source"
1852+
}
1853+
],
18361854
"label": null,
18371855
"name": "BWA-MEM2",
18381856
"outputs": [
@@ -1859,15 +1877,15 @@
18591877
"output_name": "bam_output"
18601878
}
18611879
},
1862-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4",
1880+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0",
18631881
"tool_shed_repository": {
1864-
"changeset_revision": "bec6ba059ded",
1882+
"changeset_revision": "af91699b8d4c",
18651883
"name": "bwa_mem2",
18661884
"owner": "iuc",
18671885
"tool_shed": "toolshed.g2.bx.psu.edu"
18681886
},
18691887
"tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"full\", \"__current_case__\": 4, \"algorithmic_options\": {\"algorithmic_options_selector\": \"set\", \"__current_case__\": 0, \"k\": \"19\", \"w\": \"100\", \"d\": \"100\", \"r\": \"1.5\", \"y\": \"20\", \"c\": \"500\", \"D\": \"0.5\", \"W\": \"0\", \"m\": \"50\", \"S\": true, \"P\": true, \"e\": false}, \"scoring_options\": {\"scoring_options_selector\": \"do_not_set\", \"__current_case__\": 1}, \"io_options\": {\"io_options_selector\": \"set\", \"__current_case__\": 0, \"five\": true, \"q\": false, \"T\": \"30\", \"h\": \"5\", \"a\": false, \"C\": false, \"V\": false, \"Y\": false, \"M\": false, \"K\": null}}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": null}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"set_id_auto\", \"__current_case__\": 2}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
1870-
"tool_version": "2.2.1+galaxy4",
1888+
"tool_version": "2.3+galaxy0",
18711889
"type": "tool",
18721890
"uuid": "45d2eaea-40f9-461e-bfb0-cadd9b9738b8",
18731891
"when": null,
@@ -1881,7 +1899,7 @@
18811899
},
18821900
"6": {
18831901
"annotation": "",
1884-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2",
1902+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0",
18851903
"errors": null,
18861904
"id": 6,
18871905
"input_connections": {
@@ -1890,7 +1908,16 @@
18901908
"output_name": "bam_output"
18911909
}
18921910
},
1893-
"inputs": [],
1911+
"inputs": [
1912+
{
1913+
"description": "runtime parameter for tool Samtools merge",
1914+
"name": "bed_file"
1915+
},
1916+
{
1917+
"description": "runtime parameter for tool Samtools merge",
1918+
"name": "headerbam"
1919+
}
1920+
],
18941921
"label": null,
18951922
"name": "Samtools merge",
18961923
"outputs": [
@@ -1912,15 +1939,15 @@
19121939
"output_name": "output"
19131940
}
19141941
},
1915-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2",
1942+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0",
19161943
"tool_shed_repository": {
1917-
"changeset_revision": "cae2794d2deb",
1944+
"changeset_revision": "a7617eb92baf",
19181945
"name": "samtools_merge",
19191946
"owner": "iuc",
19201947
"tool_shed": "toolshed.g2.bx.psu.edu"
19211948
},
19221949
"tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
1923-
"tool_version": "1.20+galaxy2",
1950+
"tool_version": "1.21+galaxy0",
19241951
"type": "tool",
19251952
"uuid": "f536be00-adc2-4f1f-a167-f3fd44466290",
19261953
"when": null,
@@ -1934,7 +1961,7 @@
19341961
}
19351962
},
19361963
"tags": [],
1937-
"uuid": "52451b6f-5046-4926-b61e-a16cae121c1e"
1964+
"uuid": "711463e5-023e-46c2-aa91-4a7037fe04cc"
19381965
},
19391966
"tool_id": null,
19401967
"type": "subworkflow",
@@ -2022,7 +2049,7 @@
20222049
},
20232050
"18": {
20242051
"annotation": "",
2025-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0",
2052+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.5+galaxy0",
20262053
"errors": null,
20272054
"id": 18,
20282055
"input_connections": {
@@ -2057,15 +2084,15 @@
20572084
"output_name": "default"
20582085
}
20592086
},
2060-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0",
2087+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.5+galaxy0",
20612088
"tool_shed_repository": {
2062-
"changeset_revision": "a019807f4e67",
2089+
"changeset_revision": "8511b6d85fc7",
20632090
"name": "seqtk",
20642091
"owner": "iuc",
20652092
"tool_shed": "toolshed.g2.bx.psu.edu"
20662093
},
20672094
"tool_state": "{\"P\": false, \"d\": \"2000\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"m\": {\"__class__\": \"ConnectedValue\"}, \"p\": \"1\", \"s\": \"300\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
2068-
"tool_version": "1.4+galaxy0",
2095+
"tool_version": "1.5+galaxy0",
20692096
"type": "tool",
20702097
"uuid": "05b5803e-b3ce-4c33-bfc5-23925529052e",
20712098
"when": null,
@@ -2092,7 +2119,16 @@
20922119
"output_name": "data_param"
20932120
}
20942121
},
2095-
"inputs": [],
2122+
"inputs": [
2123+
{
2124+
"description": "runtime parameter for tool Map with minimap2",
2125+
"name": "fastq_input"
2126+
},
2127+
{
2128+
"description": "runtime parameter for tool Map with minimap2",
2129+
"name": "reference_source"
2130+
}
2131+
],
20962132
"label": null,
20972133
"name": "Map with minimap2",
20982134
"outputs": [
@@ -2166,7 +2202,7 @@
21662202
},
21672203
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
21682204
"tool_shed_repository": {
2169-
"changeset_revision": "c6cec5ab35c1",
2205+
"changeset_revision": "0346286a3b0a",
21702206
"name": "pretext_map",
21712207
"owner": "iuc",
21722208
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2222,7 +2258,7 @@
22222258
},
22232259
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
22242260
"tool_shed_repository": {
2225-
"changeset_revision": "c6cec5ab35c1",
2261+
"changeset_revision": "0346286a3b0a",
22262262
"name": "pretext_map",
22272263
"owner": "iuc",
22282264
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2411,7 +2447,12 @@
24112447
"output_name": "alignment_output"
24122448
}
24132449
},
2414-
"inputs": [],
2450+
"inputs": [
2451+
{
2452+
"description": "runtime parameter for tool bedtools Genome Coverage",
2453+
"name": "input_type"
2454+
}
2455+
],
24152456
"label": null,
24162457
"name": "bedtools Genome Coverage",
24172458
"outputs": [
@@ -2549,7 +2590,7 @@
25492590
},
25502591
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
25512592
"tool_shed_repository": {
2552-
"changeset_revision": "408ece2e4647",
2593+
"changeset_revision": "936a1edffce8",
25532594
"name": "pretext_graph",
25542595
"owner": "iuc",
25552596
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2598,7 +2639,7 @@
25982639
},
25992640
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
26002641
"tool_shed_repository": {
2601-
"changeset_revision": "408ece2e4647",
2642+
"changeset_revision": "936a1edffce8",
26022643
"name": "pretext_graph",
26032644
"owner": "iuc",
26042645
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2766,7 +2807,12 @@
27662807
"output_name": "text_param"
27672808
}
27682809
},
2769-
"inputs": [],
2810+
"inputs": [
2811+
{
2812+
"description": "runtime parameter for tool Map parameter value",
2813+
"name": "input_param_type"
2814+
}
2815+
],
27702816
"label": "False if telomere track is empty",
27712817
"name": "Map parameter value",
27722818
"outputs": [
@@ -2841,7 +2887,7 @@
28412887
},
28422888
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
28432889
"tool_shed_repository": {
2844-
"changeset_revision": "408ece2e4647",
2890+
"changeset_revision": "936a1edffce8",
28452891
"name": "pretext_graph",
28462892
"owner": "iuc",
28472893
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2894,7 +2940,7 @@
28942940
},
28952941
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
28962942
"tool_shed_repository": {
2897-
"changeset_revision": "408ece2e4647",
2943+
"changeset_revision": "936a1edffce8",
28982944
"name": "pretext_graph",
28992945
"owner": "iuc",
29002946
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -3041,7 +3087,7 @@
30413087
},
30423088
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
30433089
"tool_shed_repository": {
3044-
"changeset_revision": "408ece2e4647",
3090+
"changeset_revision": "936a1edffce8",
30453091
"name": "pretext_graph",
30463092
"owner": "iuc",
30473093
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -3090,7 +3136,7 @@
30903136
},
30913137
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
30923138
"tool_shed_repository": {
3093-
"changeset_revision": "408ece2e4647",
3139+
"changeset_revision": "936a1edffce8",
30943140
"name": "pretext_graph",
30953141
"owner": "iuc",
30963142
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -3148,7 +3194,7 @@
31483194
},
31493195
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
31503196
"tool_shed_repository": {
3151-
"changeset_revision": "408ece2e4647",
3197+
"changeset_revision": "936a1edffce8",
31523198
"name": "pretext_graph",
31533199
"owner": "iuc",
31543200
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -3212,7 +3258,7 @@
32123258
},
32133259
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0",
32143260
"tool_shed_repository": {
3215-
"changeset_revision": "408ece2e4647",
3261+
"changeset_revision": "936a1edffce8",
32163262
"name": "pretext_graph",
32173263
"owner": "iuc",
32183264
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -3232,7 +3278,7 @@
32323278
},
32333279
"41": {
32343280
"annotation": "",
3235-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0",
3281+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0",
32363282
"errors": null,
32373283
"id": 41,
32383284
"input_connections": {
@@ -3261,23 +3307,23 @@
32613307
"output_name": "pretext_snap_out"
32623308
}
32633309
},
3264-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0",
3310+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0",
32653311
"tool_shed_repository": {
3266-
"changeset_revision": "26f2fe7e53a1",
3312+
"changeset_revision": "9ec9c22767c8",
32673313
"name": "pretext_snapshot",
32683314
"owner": "iuc",
32693315
"tool_shed": "toolshed.g2.bx.psu.edu"
32703316
},
32713317
"tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"yes\", \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"2000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
3272-
"tool_version": "0.0.4+galaxy0",
3318+
"tool_version": "0.0.5+galaxy0",
32733319
"type": "tool",
32743320
"uuid": "f453794e-4045-4602-9f49-26abf7f1426f",
32753321
"when": null,
32763322
"workflow_outputs": []
32773323
},
32783324
"42": {
32793325
"annotation": "",
3280-
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0",
3326+
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0",
32813327
"errors": null,
32823328
"id": 42,
32833329
"input_connections": {
@@ -3306,15 +3352,15 @@
33063352
"output_name": "pretext_snap_out"
33073353
}
33083354
},
3309-
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0",
3355+
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.5+galaxy0",
33103356
"tool_shed_repository": {
3311-
"changeset_revision": "26f2fe7e53a1",
3357+
"changeset_revision": "9ec9c22767c8",
33123358
"name": "pretext_snapshot",
33133359
"owner": "iuc",
33143360
"tool_shed": "toolshed.g2.bx.psu.edu"
33153361
},
33163362
"tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": \"yes\", \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"2000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
3317-
"tool_version": "0.0.4+galaxy0",
3363+
"tool_version": "0.0.5+galaxy0",
33183364
"type": "tool",
33193365
"uuid": "533b33d8-3a3b-480a-9978-1526d65606c5",
33203366
"when": null,
@@ -3430,6 +3476,7 @@
34303476
}
34313477
},
34323478
"tags": [],
3433-
"uuid": "34226708-cba3-421c-809f-6ba105b3812c",
3434-
"version": 4
3479+
"uuid": "8406beb7-388a-4d5f-b248-62b618a93420",
3480+
"version": 1,
3481+
"release": "1.0b7"
34353482
}

0 commit comments

Comments
 (0)