Skip to content

Updating workflows/epigenetics/hic-hicup-cooler from 0.3 to 0.4 #971

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Updating workflows/epigenetics/hic-hicup-cooler from 0.3 to 0.4 #971

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions workflows/epigenetics/hic-hicup-cooler/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.4] - 2025-10-06

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0`

## [0.3] - 2023-09-08

### Update tools
Expand Down
116 changes: 76 additions & 40 deletions workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler.ga
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
{
"a_galaxy_workflow": "true",
"annotation": "End-to-end processing of Capture Hi-C paired-end sequencing data. Transforms raw FASTQ files into balanced contact matrices using HiCUP for processing Hi-C reads (adapter trimming, mapping, filtering for valid pairs) with additional filtering for MAPQ and captured regions. The workflow generates sorted tabix files via cooler and produces balanced cool files at user-specified resolution for downstream analysis and visualization.",
"comments": [],
"creator": [
{
"class": "Person",
Expand All @@ -10,7 +11,6 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.3",
"name": "Capture Hi-C Processing: FASTQ to Balanced Cool Files",
"steps": {
"0": {
Expand All @@ -33,7 +33,7 @@
"top": 39.12167999999406
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\", \"fields\": null}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "30fe3d0f-541a-478a-b57d-a43c0c16ccad",
Expand All @@ -60,7 +60,7 @@
"top": 109.12167999999406
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "45194ed6-a1e9-4248-8d3a-f51febc36d61",
Expand All @@ -87,7 +87,7 @@
"top": 184.12167999999406
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "ec011ceb-c601-464f-8661-ca9c0b335bb5",
Expand All @@ -114,7 +114,7 @@
"top": 269.62167999999406
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "11e64d82-c022-48b2-b616-076bfcdb14ad",
Expand All @@ -141,7 +141,7 @@
"top": 339.12167999999406
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "748c8800-5bef-41b7-b2cf-6d6a57c0eb70",
Expand All @@ -168,7 +168,7 @@
"top": 409.62167999999406
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "1e019ddf-171c-4247-ab11-0d2cdbe10f6a",
Expand All @@ -195,7 +195,7 @@
"top": 473.87167999999406
},
"tool_id": null,
"tool_state": "{\"restrictions\": [\"\", \"--cis-only\", \"--trans-only\"], \"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"restrictions\": [\"\", \"--cis-only\", \"--trans-only\"], \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "2cf7902e-aa51-45a7-ae75-9107bbb41911",
Expand All @@ -222,7 +222,7 @@
"top": 622.6216799999941
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "386a8e30-aab6-4168-877e-581b883928e5",
Expand All @@ -249,7 +249,7 @@
"top": 723.6216799999941
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "47de292d-7499-407e-bf9a-b67a4dc47348",
Expand All @@ -276,7 +276,7 @@
"top": 835.6216799999941
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "25480973-63be-4e64-9ba1-26088b4a65c4",
Expand Down Expand Up @@ -324,6 +324,7 @@
"subworkflow": {
"a_galaxy_workflow": "true",
"annotation": "",
"comments": [],
"creator": [
{
"class": "Person",
Expand Down Expand Up @@ -355,7 +356,7 @@
"top": 12.5
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\", \"fields\": null}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "30fe3d0f-541a-478a-b57d-a43c0c16ccad",
Expand All @@ -382,7 +383,7 @@
"top": 82.5
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "45194ed6-a1e9-4248-8d3a-f51febc36d61",
Expand All @@ -409,7 +410,7 @@
"top": 155.5
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "ec011ceb-c601-464f-8661-ca9c0b335bb5",
Expand All @@ -436,7 +437,7 @@
"top": 248.5
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "c807fdbf-1c1d-45b4-851e-47fb919b07d6",
Expand All @@ -463,7 +464,7 @@
"top": 320.5
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "748c8800-5bef-41b7-b2cf-6d6a57c0eb70",
Expand Down Expand Up @@ -497,7 +498,20 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Hicup Pipeline",
"name": "advanced_options"
},
{
"description": "runtime parameter for tool Hicup Pipeline",
"name": "library"
},
{
"description": "runtime parameter for tool Hicup Pipeline",
"name": "reference_genome"
}
],
"label": "HiCUP",
"name": "Hicup Pipeline",
"outputs": [
Expand Down Expand Up @@ -646,7 +660,12 @@
"output_name": "dataset_hicup"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Hicup to juicer converter",
"name": "digester"
}
],
"label": "valid pairs in juicebox format",
"name": "Hicup to juicer converter",
"outputs": [
Expand Down Expand Up @@ -740,8 +759,8 @@
]
}
},
"tags": "",
"uuid": "9df7c037-6fe4-47e9-8311-e40bc5101b58"
"tags": [],
"uuid": "6657d1d2-3bdc-474b-a580-df1653490bd8"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -946,7 +965,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool cooler csort with tabix",
"name": "size_source"
}
],
"label": "Sort filtered pairs and index",
"name": "cooler csort with tabix",
"outputs": [
Expand Down Expand Up @@ -977,7 +1001,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_csort_tabix/cooler_csort_tabix/0.9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "8c3cba559c99",
"changeset_revision": "026950a1853c",
"name": "cooler_csort_tabix",
"owner": "lldelisle",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1031,6 +1055,7 @@
"subworkflow": {
"a_galaxy_workflow": "true",
"annotation": "",
"comments": [],
"creator": [
{
"class": "Person",
Expand Down Expand Up @@ -1062,7 +1087,7 @@
"top": 33.5
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "d0a82863-82f8-426c-addb-06066e9d0a73",
Expand Down Expand Up @@ -1095,7 +1120,7 @@
"top": 123.5
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "48506f80-b1b5-4d1d-98a6-c6882de026f1",
Expand Down Expand Up @@ -1128,7 +1153,7 @@
"top": 208.25
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "588962a4-8ce4-4929-81fd-a9dfdd032598",
Expand All @@ -1155,7 +1180,7 @@
"top": 309.75
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "d6375500-a591-47a9-b126-950347e3e7a8",
Expand Down Expand Up @@ -1183,7 +1208,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool cooler_makebins",
"name": "size_source"
}
],
"label": "make bed with bins",
"name": "cooler_makebins",
"outputs": [
Expand All @@ -1205,7 +1235,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_makebins/cooler_makebins/0.9.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "ebd2a52eb245",
"changeset_revision": "3df254580b06",
"name": "cooler_makebins",
"owner": "lldelisle",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1236,7 +1266,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool cooler_cload_tabix",
"name": "format_sel"
}
],
"label": "Load pairs in matrix",
"name": "cooler_cload_tabix",
"outputs": [
Expand All @@ -1260,7 +1295,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/0.9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "0641e1c892c6",
"changeset_revision": "168e86e96afa",
"name": "cooler_cload_tabix",
"owner": "lldelisle",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1322,7 +1357,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_balance/cooler_balance/0.9.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "8f9fe0667b89",
"changeset_revision": "b387933e4d3d",
"name": "cooler_balance",
"owner": "lldelisle",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand All @@ -1341,8 +1376,8 @@
]
}
},
"tags": "",
"uuid": "1a6f4422-8f82-4444-a30c-bde38d181e41"
"tags": [],
"uuid": "676022aa-315d-4dd5-be9e-a7a70cb0178f"
},
"tool_id": null,
"type": "subworkflow",
Expand All @@ -1363,7 +1398,7 @@
},
"16": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0",
"errors": null,
"id": 16,
"input_connections": {
Expand Down Expand Up @@ -1398,15 +1433,15 @@
"output_name": "outFileName"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0",
"tool_shed_repository": {
"changeset_revision": "59fd173ac850",
"changeset_revision": "86d0ebe09628",
"name": "pygenometracks",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"global_args\": {\"title\": \"\", \"fontsize\": \"12\", \"dpi\": \"72\", \"width\": \"40.0\", \"plotWidth\": null, \"height\": null, \"trackLabelFraction\": \"0.05\", \"trackLabelHAlign\": \"left\", \"decreasingXAxis\": false}, \"image_file_format\": \"png\", \"region\": {\"__class__\": \"ConnectedValue\"}, \"tracks\": [{\"__index__\": 0, \"track_file_style_conditional\": {\"track_file_style_selector\": \"hic_matrix_option\", \"__current_case__\": 0, \"title\": \"\", \"matrix_h5_cooler_multiple\": {\"__class__\": \"ConnectedValue\"}, \"colormap\": \"RdYlBu_r\", \"min_value\": null, \"max_value\": null, \"depth\": \"8000000\", \"transform\": \"no\", \"height_matrix\": null, \"show_masked_bins\": false, \"boundaries_file\": {\"__class__\": \"RuntimeValue\"}, \"scale_factor\": \"1.0\", \"rasterize\": true, \"invert_orientation\": false, \"spacer_height\": null}}, {\"__index__\": 1, \"track_file_style_conditional\": {\"track_file_style_selector\": \"xaxis_option\", \"__current_case__\": 13, \"title\": \"\", \"fontsize\": null, \"xaxis_where\": \"bottom\", \"spacer_height\": null}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.8+galaxy2",
"tool_version": "3.9+galaxy0",
"type": "tool",
"uuid": "dfbe45de-b2a7-479e-b717-29ec5b31379e",
"when": null,
Expand All @@ -1422,6 +1457,7 @@
"tags": [
"Hi-C"
],
"uuid": "2a89cbe4-a69f-4bff-9465-2e04b0217e35",
"version": 4
}
"uuid": "858f36e1-c9b9-4ca6-b1a9-07708594d13c",
"version": 1,
"release": "0.4"
}
Loading
Loading