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a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -1,165 +1,300 @@ { "a_galaxy_workflow": "true", "annotation": "", - "comments": [], + "comments": [ + { + "child_steps": [ + 33, + 35, + 36 + ], + "color": "orange", + "data": { + "title": "Add tracks to the Hi-C map" + }, + "id": 6, + "position": [ + 2873.0455874099634, + 621.8 + ], + "size": [ + 861.8, + 613.8 + ], + "type": "frame" + }, + { + "child_steps": [ + 22, + 18, + 15, + 10, + 16, + 11, + 19 + ], + "color": "blue", + "data": { + "title": "Merge Haplotypes" + }, + "id": 0, + "position": [ + 424.0455874099634, + 0.0 + ], + "size": [ + 1283.3, + 768.6 + ], + "type": "frame" + }, + { + "child_steps": [ + 12, + 17, + 13, + 20, + 21 + ], + "color": "yellow", + "data": { + "title": "Optionnal: Trim Hi-C reads" + }, + "id": 1, + "position": [ + 733.2455874099634, + 811.4 + ], + "size": [ + 1168.5, + 515.8 + ], + "type": "frame" + }, 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URL)", + "name": "PretextMap Generation with bed files", "report": { "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" }, "steps": { "0": { - "annotation": "suffix added to contigs belonging to haplotype 1. 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"35": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, - "id": 35, + "id": 37, "input_connections": { "input": { - "id": 34, + "id": 36, "output_name": "graph_out" } }, @@ -1593,8 +1797,8 @@ } ], "position": { - "left": 3699.3145719636714, - "top": 475.13330078125 + "left": 3779.397785516864, + "top": 996.3016559858406 }, "post_job_actions": { "RenameDatasetActionpretext_snap_out": { @@ -1634,6 +1838,6 @@ } }, "tags": [], - "uuid": "14d25f8d-58f0-4ad9-ba5e-68514d9a81b3", - "version": 23 -} \ No newline at end of file + "uuid": "83871ed6-a664-40f4-8018-968a561f7c14", + "version": 8 +} From 4e20b69ceeaa2d5e46b19cec774a5ac5a2711465 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 12 Nov 2024 11:39:37 -0500 Subject: [PATCH 03/27] add license, authors, and diverse labels and tags --- .../PretextMap_Generation.ga | 1079 ++++++++++------- 1 file changed, 617 insertions(+), 462 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga index 156009bd5..da01f3f69 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -4,34 +4,13 @@ "comments": [ { "child_steps": [ - 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30 + 31 ], "color": "lime", "data": { @@ -113,50 +116,67 @@ }, { "child_steps": [ - 24, - 25, - 29, + 14, + 27, 32 ], - "color": "red", + "color": "green", "data": { - "title": "Generate Hi-C map" + "title": "Coverage" }, - "id": 3, + "id": 5, "position": [ - 2008.6455874099634, - 489.2 + 1881.7455874099635, + 1453.3 ], "size": [ - 779.6, - 512.7 + 833.6, + 266.8 ], "type": "frame" }, { "child_steps": [ - 31, - 27, - 14 + 35, + 36, + 37 ], - "color": "green", + "color": "orange", "data": { - "title": "Coverage" + "title": "Add tracks to the Hi-C map" }, - "id": 5, + "id": 6, "position": [ - 1881.7455874099635, - 1453.3 + 2873.0455874099634, + 621.8 ], "size": [ - 833.6, - 266.8 + 861.8, + 613.8 ], "type": "frame" } ], + "creator": [ + { + "class": "Person", + "identifier": "0000-0001-6228-2785", + "name": "Patrik Smeds" + }, + { + "class": "Organization", + "name": "Galaxy" + }, + { + "class": "Person", + "identifier": "0000-0001-6421-3484", + "name": "Delphine Lariviere" + } + ], "format-version": "0.1", - 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"tool_version": "0.0.3+galaxy1", - "type": "tool", - "uuid": "031f094c-6568-4447-94c2-731a2e7d64db", - "when": null, - "workflow_outputs": [ - { - "label": "Pretext Snapshot", - "output_name": "pretext_snap_out", - "uuid": "01341371-3d55-43bb-bb00-cca206896002" - } - ] - }, - "35": { + "36": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", "errors": null, - "id": 35, + "id": 36, "input_connections": { "input": { - "id": 30, + "id": 31, "output_name": "data_param" }, "pretext": { - "id": 33, + "id": 35, "output_name": "graph_out" } }, @@ -1719,18 +1867,18 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", "errors": null, - "id": 36, + "id": 37, "input_connections": { "input": { - "id": 28, + "id": 30, "output_name": "out_file1" }, "pretext": { - "id": 35, + "id": 36, "output_name": "graph_out" } }, @@ -1754,6 +1902,13 @@ }, "action_type": "RenameDatasetAction", "output_name": "graph_out" + }, + "TagDatasetActiongraph_out": { + "action_arguments": { + "tags": "pretext_all_tracks" + }, + "action_type": "TagDatasetAction", + "output_name": "graph_out" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", @@ -1776,14 +1931,14 @@ } ] }, - "37": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, - "id": 37, + "id": 38, "input_connections": { "input": { - "id": 36, + "id": 37, "output_name": "graph_out" } }, @@ -1838,6 +1993,6 @@ } }, "tags": [], - "uuid": "83871ed6-a664-40f4-8018-968a561f7c14", - "version": 8 -} + "uuid": "89e2a0ab-6ad3-480a-b611-63f497e9b6c7", + "version": 16 +} \ No newline at end of file From b666689c65fe8c3f070bfaa99298e0a0403a9e7e Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 12 Nov 2024 12:15:09 -0500 Subject: [PATCH 04/27] change telomere track height to correspond to the size of the telomeres --- .../PretextMap_Generation.ga | 258 +++++++++++------- 1 file changed, 165 insertions(+), 93 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga index da01f3f69..4501830b3 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -29,26 +29,23 @@ }, { "child_steps": [ - 12, - 13, - 17, - 18, - 21, - 23, - 24 + 33, + 35, + 28, + 29 ], - "color": "yellow", + "color": "red", "data": { - "title": "Optionnal: Trim Hi-C reads" + "title": "Generate Hi-C map" }, - "id": 1, + "id": 3, "position": [ - 698.7, - 815 + 2008.6455874099634, + 489.2 ], "size": [ - 1168.5, - 515.8 + 779.6, + 512.7 ], "type": "frame" }, @@ -74,29 +71,33 @@ }, { "child_steps": [ - 28, - 29, - 33, - 34 + 12, + 13, + 17, + 18, + 21, + 23, + 24 ], - "color": "red", + "color": "yellow", "data": { - "title": "Generate Hi-C map" + "title": "Optionnal: Trim Hi-C reads" }, - "id": 3, + "id": 1, "position": [ - 2008.6455874099634, - 489.2 + 698.7, + 815 ], "size": [ - 779.6, - 512.7 + 1168.5, + 515.8 ], "type": "frame" }, { "child_steps": [ 26, + 34, 31 ], "color": "lime", @@ -109,8 +110,8 @@ 1088.7 ], "size": [ - 584.3, - 248.8 + 761, + 296 ], "type": "frame" }, @@ -137,9 +138,9 @@ }, { "child_steps": [ - 35, 36, - 37 + 37, + 38 ], "color": "orange", "data": { @@ -260,7 +261,13 @@ "type": "parameter_input", "uuid": "742c987a-a4b8-4208-918a-cfb4bd55cd66", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d4f1ec43-e160-424d-83df-e192d19db235" + } + ] }, "3": { "annotation": "Suffix added to scaffolds belonging to haplotype 1. ", @@ -287,7 +294,13 @@ "type": "parameter_input", "uuid": "f61b5666-fa76-4892-9b1d-d31979bc5a44", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2d7ba9c8-64bd-4c9c-8ebd-1fe9d8b77f70" + } + ] }, "4": { "annotation": "Suffix added to contigs belonging to haplotype 2. ", @@ -314,7 +327,13 @@ "type": "parameter_input", "uuid": "294ab686-1b84-4a79-aa5c-10553af61911", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6bb04b2f-0c0d-4225-bbb1-d8a2c0252c6b" + } + ] }, "5": { "annotation": "", @@ -395,7 +414,13 @@ "type": "parameter_input", "uuid": "6d1391db-7fef-4b5c-a236-26016d6d0aab", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "edd62f76-a21a-4d23-a447-aa40acde8668" + } + ] }, "8": { "annotation": "", @@ -422,7 +447,13 @@ "type": "parameter_input", "uuid": "84c91e14-1709-4602-8771-eea1dadf471b", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "81dd3672-732e-452c-9f30-5eac21a7dd28" + } + ] }, "9": { "annotation": "For coverage. MUST be fastqsanger. 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", @@ -1287,8 +1318,8 @@ } ], "position": { - "left": 2069.8354714501575, - "top": 1130.757810358141 + "left": 2066.8984375, + "top": 1130.7578125 }, "post_job_actions": { "RenameDatasetActiondefault": { @@ -1297,13 +1328,6 @@ }, "action_type": "RenameDatasetAction", "output_name": "default" - }, - "TagDatasetActiondefault": { - "action_arguments": { - "tags": "telomeres" - }, - "action_type": "TagDatasetAction", - "output_name": "default" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_telo/1.4+galaxy0", @@ -1494,8 +1518,8 @@ } ], "position": { - "left": 2109.7128338205225, - "top": 86.22655330659961 + "left": 2109.7109749180486, + "top": 86.46925811943585 }, "post_job_actions": { "ChangeDatatypeActionout_file1": { @@ -1542,53 +1566,34 @@ }, "31": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "content_id": "Cut1", "errors": null, "id": 31, "input_connections": { - "style_cond|type_cond|pick_from_0|value": { + "input": { "id": 26, "output_name": "default" } }, "inputs": [], "label": null, - "name": "Pick parameter value", + "name": "Cut", "outputs": [ { - "name": "data_param", - "type": "input" + "name": "out_file1", + "type": "tabular" } ], "position": { - "left": 2347.5364440015765, - "top": 1163.0197194412294 - }, - "post_job_actions": { - "ChangeDatatypeActiondata_param": { - "action_arguments": { - "newtype": "bedgraph" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "data_param" - }, - "HideDatasetActiondata_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "data_param" - } + "left": 2297.854521975427, + "top": 1273.1224894147651 }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", - "tool_shed_repository": { - "changeset_revision": "b19e21af9c52", - "name": "pick_value", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"style_cond\": {\"pick_style\": \"only\", \"__current_case__\": 3, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"35": { + "36": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", "errors": null, - "id": 35, + "id": 36, "input_connections": { "input": { "id": 32, "output_name": "outFileName" }, "pretext": { - "id": 34, + "id": 35, "output_name": "pretext_map_out" } }, @@ -1818,18 +1890,18 @@ "when": null, "workflow_outputs": [] }, - "36": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", "errors": null, - "id": 36, + "id": 37, "input_connections": { "input": { - "id": 31, - "output_name": "data_param" + "id": 34, + "output_name": "out_file1" }, "pretext": { - "id": 35, + "id": 36, "output_name": "graph_out" } }, @@ -1867,18 +1939,18 @@ "when": null, "workflow_outputs": [] }, - "37": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.6+galaxy0", "errors": null, - "id": 37, + "id": 38, "input_connections": { "input": { "id": 30, "output_name": "out_file1" }, "pretext": { - "id": 36, + "id": 37, "output_name": "graph_out" } }, @@ -1931,14 +2003,14 @@ } ] }, - "38": { + "39": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, - "id": 38, + "id": 39, "input_connections": { "input": { - "id": 37, + "id": 38, "output_name": "graph_out" } }, @@ -1993,6 +2065,6 @@ } }, "tags": [], - "uuid": "89e2a0ab-6ad3-480a-b611-63f497e9b6c7", - "version": 16 + "uuid": "b2858d48-25a5-485f-beb6-78564409d6d7", + "version": 17 } \ No newline at end of file From 42a724076631ab4208ebb5707c5ec77f9c5dc5f2 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 12 Nov 2024 15:11:00 -0500 Subject: [PATCH 05/27] Add README and CHANGELOG --- .../Curation-TreeValGal/CHANGELOG.md | 5 ++++ .../Curation-TreeValGal/README.md | 30 +++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md create mode 100644 workflows/VGP-assembly-v2/Curation-TreeValGal/README.md diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md b/workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md new file mode 100644 index 000000000..73254a9db --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [1.0] 2024-11-12 + +- Creation of a workflow for the generation of Hi-C Maps with coverage, gaps and Telomere Tracks \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md new file mode 100644 index 000000000..80cbbd619 --- /dev/null +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md @@ -0,0 +1,30 @@ +# PretextMap generation + +This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies. + + +## Inputs + +1. **Haplotype 1** [fasta] +2. **Haplotype 2** [fasta] +3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information. +4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. +5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. +6. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads +7. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads +8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". +9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. +10. **PacBio reads collection** [fastq] Collection of PacBio reads. + + +## Outputs + +1. Concatenated Assembly [fasta] +2. Trimmed Hi-C data (If trimming option is selected) [fastq] +3. Mapped Hi-C reads [bam] +4. Telomeres track [bedgraph] +5. Gap track [bedgraph] +6. Coverage track [bigwig] +7. Pretext Map without tracks [pretext] +8. Pretext Map with tracks [pretext] +9. Pretext Snapshot image of the Hi-C contact map [png] \ No newline at end of file From e6c4591812e6ed29eea759619b8aa03d9f78ed4f Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 14 Nov 2024 11:23:15 -0500 Subject: [PATCH 06/27] update pretextgraph to fix track display issue, and add parameters to go around the fasta implicit conversion problem --- .../PretextMap_Generation.ga | 1371 ++++++++++------- 1 file changed, 802 insertions(+), 569 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga index 4501830b3..6ca641dd4 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -4,13 +4,13 @@ "comments": [ { "child_steps": [ - 10, - 11, - 15, - 16, - 19, - 20, - 22 + 13, + 14, + 22, + 23, + 25, + 26, + 29 ], "color": "blue", "data": { @@ -18,41 +18,44 @@ }, "id": 0, "position": [ - 424.0455874099634, - 0 + 354.6656953811405, + 335.94283916537546 ], "size": [ - 1283.3, - 768.6 + 1283, + 769 ], "type": "frame" }, { "child_steps": [ - 33, - 35, - 28, - 29 + 15, + 16, + 20, + 21, + 24, + 27, + 28 ], - "color": "red", + "color": "yellow", "data": { - "title": "Generate Hi-C map" + "title": "Optionnal: Trim Hi-C reads" }, - "id": 3, + "id": 1, "position": [ - 2008.6455874099634, - 489.2 + 986.4656953811406, + 1152.4428391653755 ], "size": [ - 779.6, - 512.7 + 1168.5, + 515.8 ], "type": "frame" }, { "child_steps": [ - 25, - 30 + 30, + 35 ], "color": "turquoise", "data": { @@ -60,8 +63,8 @@ }, "id": 2, "position": [ - 1837.8455874099634, - 29.80000000000001 + 2125.611282791104, + 367.24283916537547 ], "size": [ 541.9, @@ -71,55 +74,51 @@ }, { "child_steps": [ - 12, - 13, - 17, - 18, - 21, - 23, - 24 + 33, + 40, + 37 ], - "color": "yellow", + "color": "lime", "data": { - "title": "Optionnal: Trim Hi-C reads" + "title": "Telomeres" }, - "id": 1, + "id": 4, "position": [ - 698.7, - 815 + 2314.611282791104, + 1426.1428391653753 ], "size": [ - 1168.5, - 515.8 + 761, + 296 ], "type": "frame" }, { "child_steps": [ - 26, - 34, - 31 + 41, + 42, + 43 ], - "color": "lime", + "color": "orange", "data": { - "title": "Telomeres" + "title": "Add tracks to the Hi-C map" }, - "id": 4, + "id": 6, "position": [ - 2026.8455874099634, - 1088.7 + 3160.811282791104, + 959.2428391653755 ], "size": [ - 761, - 296 + 861.8, + 613.8 ], "type": "frame" }, { "child_steps": [ - 14, - 27, - 32 + 17, + 34, + 38 ], "color": "green", "data": { @@ -127,8 +126,8 @@ }, "id": 5, "position": [ - 1881.7455874099635, - 1453.3 + 2169.511282791104, + 1790.7428391653752 ], "size": [ 833.6, @@ -138,22 +137,23 @@ }, { "child_steps": [ + 31, + 32, 36, - 37, - 38 + 39 ], - "color": "orange", + "color": "red", "data": { - "title": "Add tracks to the Hi-C map" + "title": "Generate Hi-C map" }, - "id": 6, + "id": 3, "position": [ - 2873.0455874099634, - 621.8 + 2296.411282791104, + 826.6428391653754 ], "size": [ - 861.8, - 613.8 + 779.6, + 512.7 ], "type": "frame" } @@ -191,15 +191,15 @@ "inputs": [ { "description": "fasta file for haplotype 1", - "name": "haplotype 1" + "name": "Haplotype 1" } ], - "label": "haplotype 1", + "label": "Haplotype 1", "name": "Input dataset", "outputs": [], "position": { "left": 0, - "top": 95.43488222704909 + "top": 333.95847137710746 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -218,15 +218,15 @@ "inputs": [ { "description": "fasta file for haplotype 2\n", - "name": "haplotype 2" + "name": "Haplotype 2" } ], - "label": "haplotype 2", + "label": "Haplotype 2", "name": "Input dataset", "outputs": [], "position": { - "left": 37.63468426172312, - "top": 184.6850759762522 + "left": 9.34765625, + "top": 407.02878387710746 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -237,11 +237,44 @@ "workflow_outputs": [] }, "2": { - "annotation": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", + "annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Are the fasta files compressed?" + } + ], + "label": "Are the fasta files compressed?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 22.203125, + "top": 482.34519012710746 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "e56c8e2c-7f88-403b-85ea-7a4fda8785e8", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "b591c6e4-0770-4d4b-939f-1bc66469b9a6" + } + ] + }, + "3": { + "annotation": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", + "content_id": null, + "errors": null, + "id": 3, + "input_connections": {}, "inputs": [ { "description": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", @@ -252,8 +285,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 122.04055495132593, - "top": 317.18558173251904 + "left": 31.593973006701162, + "top": 581.0978300068202 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -265,15 +298,15 @@ { "label": null, "output_name": "output", - "uuid": "d4f1ec43-e160-424d-83df-e192d19db235" + "uuid": "8a881807-95b4-4862-9846-4e0d9b3dcb58" } ] }, - "3": { + "4": { "annotation": "Suffix added to scaffolds belonging to haplotype 1. 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Use with some Arima hiC if the Hi-C map looks \"noisy\".", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { @@ -405,8 +438,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 427.9153046613911, - "top": 1264.842502067899 + "left": 715.6810000425317, + "top": 1602.2853412332743 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -418,28 +451,28 @@ { "label": null, "output_name": "output", - "uuid": "edd62f76-a21a-4d23-a447-aa40acde8668" + "uuid": "4b516f8c-177e-4f98-a814-8321d48ac3f8" } ] }, - "8": { + "9": { "annotation": "", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { "description": "", - "name": "telomere repeat to suit species." + "name": "Telomere repeat to suit species" } ], - "label": "telomere repeat to suit species.", + "label": "Telomere repeat to suit species", "name": "Input parameter", "outputs": [], "position": { - "left": 582.1830387317603, - "top": 1417.0965620390723 + "left": 869.9487341129009, + "top": 1754.5394012044476 }, "tool_id": null, "tool_state": "{\"default\": \"CCCTAA\", \"parameter_type\": \"text\", \"optional\": true}", @@ -451,28 +484,28 @@ { "label": null, "output_name": "output", - "uuid": "81dd3672-732e-452c-9f30-5eac21a7dd28" + "uuid": "5e5257ba-9346-40cc-9bba-ac680f94d9b7" } ] }, - "9": { - "annotation": "For coverage. 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"39": { + "44": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, - "id": 39, + "id": 44, "input_connections": { "input": { - "id": 38, + "id": 43, "output_name": "graph_out" } }, @@ -2024,8 +2257,8 @@ } ], "position": { - "left": 3779.397785516864, - "top": 996.3016559858406 + "left": 4067.1634808980048, + "top": 1333.7444951512161 }, "post_job_actions": { "RenameDatasetActionpretext_snap_out": { @@ -2065,6 +2298,6 @@ } }, "tags": [], - "uuid": "b2858d48-25a5-485f-beb6-78564409d6d7", - "version": 17 + "uuid": "5c513816-f9d6-46f8-87e7-8701001f20ae", + "version": 26 } \ No newline at end of file From 6cc5b239a269c68205e0297250b029d23a7b93c9 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Thu, 14 Nov 2024 11:25:21 -0500 Subject: [PATCH 07/27] add new parameter to the README --- .../VGP-assembly-v2/Curation-TreeValGal/README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md index 80cbbd619..bb432cfff 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md @@ -8,13 +8,14 @@ This workflow generates Hi-C contact maps for diploid genome assemblies in the P 1. **Haplotype 1** [fasta] 2. **Haplotype 2** [fasta] 3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information. -4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. -5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. -6. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads -7. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads -8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". -9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. -10. **PacBio reads collection** [fastq] Collection of PacBio reads. +4. **Are the fasta files compressed?** Select `yes` if the assembly files have the format [fasta.gz] +5. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. +6. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. +7. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads +8. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads +9. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". +10. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. +11. **PacBio reads collection** [fastq] Collection of PacBio reads. ## Outputs From 851f762d149142da17cf2c74fe9d9d147473e987 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 20 Nov 2024 11:29:41 -0500 Subject: [PATCH 08/27] Remove explicit data conversion, it got fixed in galaxy --- .../PretextMap_Generation.ga | 1274 +++++++---------- 1 file changed, 538 insertions(+), 736 deletions(-) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga index 6ca641dd4..9fee03f1f 100644 --- a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga @@ -4,13 +4,13 @@ "comments": [ { "child_steps": [ - 13, - 14, - 22, - 23, - 25, - 26, - 29 + 10, + 11, + 15, + 16, + 19, + 20, + 22 ], "color": "blue", "data": { @@ -19,7 +19,7 @@ "id": 0, "position": [ 354.6656953811405, - 335.94283916537546 + 1.9843677882680026 ], "size": [ 1283, @@ -29,13 +29,13 @@ }, { "child_steps": [ - 15, - 16, - 20, + 12, + 13, + 17, + 18, 21, - 24, - 27, - 28 + 23, + 24 ], "color": "yellow", "data": { @@ -44,7 +44,7 @@ "id": 1, "position": [ 986.4656953811406, - 1152.4428391653755 + 818.4843677882681 ], "size": [ 1168.5, @@ -55,7 +55,7 @@ { "child_steps": [ 30, - 35 + 25 ], "color": "turquoise", "data": { @@ -64,7 +64,7 @@ "id": 2, "position": [ 2125.611282791104, - 367.24283916537547 + 33.284367788268014 ], "size": [ 541.9, @@ -74,51 +74,52 @@ }, { "child_steps": [ + 35, 33, - 40, - 37 + 28, + 29 ], - "color": "lime", + "color": "red", "data": { - "title": "Telomeres" + "title": "Generate Hi-C map" }, - "id": 4, + "id": 3, "position": [ - 2314.611282791104, - 1426.1428391653753 + 2296.411282791104, + 492.684367788268 ], "size": [ - 761, - 296 + 779.6, + 512.7 ], "type": "frame" }, { "child_steps": [ - 41, - 42, - 43 + 26, + 34, + 31 ], - "color": "orange", + "color": "lime", "data": { - "title": "Add tracks to the Hi-C map" + "title": "Telomeres" }, - "id": 6, + "id": 4, "position": [ - 3160.811282791104, - 959.2428391653755 + 2314.611282791104, + 1092.184367788268 ], "size": [ - 861.8, - 613.8 + 761, + 296 ], "type": "frame" }, { "child_steps": [ - 17, - 34, - 38 + 32, + 14, + 27 ], "color": "green", "data": { @@ -127,7 +128,7 @@ "id": 5, "position": [ 2169.511282791104, - 1790.7428391653752 + 1456.784367788268 ], "size": [ 833.6, @@ -137,23 +138,22 @@ }, { "child_steps": [ - 31, - 32, 36, - 39 + 37, + 38 ], - "color": "red", + "color": "orange", "data": { - "title": "Generate Hi-C map" + "title": "Add tracks to the Hi-C map" }, - "id": 3, + "id": 6, "position": [ - 2296.411282791104, - 826.6428391653754 + 3160.811282791104, + 625.284367788268 ], "size": [ - 779.6, - 512.7 + 861.8, + 613.8 ], "type": "frame" } @@ -176,7 +176,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.0", "name": "PretextMap Generation from 2 haplotypes", "report": { "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" @@ -199,7 +198,7 @@ "outputs": [], "position": { "left": 0, - "top": 333.95847137710746 + "top": 0.0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -226,7 +225,7 @@ "outputs": [], "position": { "left": 9.34765625, - "top": 407.02878387710746 + "top": 73.0703125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -237,43 +236,10 @@ "workflow_outputs": [] }, "2": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "Are the fasta files compressed?" - } - ], - "label": "Are the fasta files compressed?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 22.203125, - "top": 482.34519012710746 - }, - "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "e56c8e2c-7f88-403b-85ea-7a4fda8785e8", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "b591c6e4-0770-4d4b-939f-1bc66469b9a6" - } - ] - }, - "3": { "annotation": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", "content_id": null, "errors": null, - "id": 3, + "id": 2, "input_connections": {}, "inputs": [ { @@ -286,7 +252,7 @@ "outputs": [], "position": { "left": 31.593973006701162, - "top": 581.0978300068202 + "top": 247.13935862971277 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -298,15 +264,15 @@ { "label": null, "output_name": "output", - "uuid": "8a881807-95b4-4862-9846-4e0d9b3dcb58" + "uuid": "22587979-c564-4ef6-90a6-eb9d008b1708" } ] }, - "4": { + "3": { "annotation": "Suffix added to scaffolds belonging to haplotype 1. ", "content_id": null, "errors": null, - "id": 4, + "id": 3, "input_connections": {}, "inputs": [ { @@ -319,7 +285,7 @@ "outputs": [], "position": { "left": 54.592452969330225, - "top": 727.4858587622581 + "top": 393.52738738515063 }, "tool_id": null, "tool_state": "{\"default\": \"hap1\", \"parameter_type\": \"text\", \"optional\": true}", @@ -331,15 +297,15 @@ { "label": null, "output_name": "output", - "uuid": "30cfd630-ae25-435a-89a2-0dcb12509d03" + "uuid": "7e0e37f8-6afe-4823-b126-b67121a87ae7" } ] }, - "5": { + "4": { "annotation": "Suffix added to contigs belonging to haplotype 2. ", "content_id": null, "errors": null, - "id": 5, + "id": 4, "input_connections": {}, "inputs": [ { @@ -352,7 +318,7 @@ "outputs": [], "position": { "left": 78.57474659995361, - "top": 828.0132608986686 + "top": 494.05478952156113 }, "tool_id": null, "tool_state": "{\"default\": \"hap2\", \"parameter_type\": \"text\", \"optional\": true}", @@ -364,15 +330,15 @@ { "label": null, "output_name": "output", - "uuid": "7cd4c79b-0760-41e1-b9a8-bc393d593452" + "uuid": "0addc4b7-8523-44a1-b35c-b83b3914ed63" } ] }, - "6": { + "5": { "annotation": "", "content_id": null, "errors": null, - "id": 6, + "id": 5, "input_connections": {}, "inputs": [ { @@ -385,7 +351,7 @@ "outputs": [], "position": { "left": 634.4517541662567, - "top": 1399.1982747047919 + "top": 1065.2398033276845 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -395,11 +361,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 7, + "id": 6, "input_connections": {}, "inputs": [ { @@ -412,7 +378,7 @@ "outputs": [], "position": { "left": 665.0496572173611, - "top": 1500.08891134727 + "top": 1166.1304399701626 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -422,11 +388,11 @@ "when": null, "workflow_outputs": [] }, - "8": { + "7": { "annotation": "Trim 5 bases at the end of the paired reads. Use with some Arima hiC if the Hi-C map looks \"noisy\".", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -439,7 +405,7 @@ "outputs": [], "position": { "left": 715.6810000425317, - "top": 1602.2853412332743 + "top": 1268.326869856167 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -451,15 +417,15 @@ { "label": null, "output_name": "output", - "uuid": "4b516f8c-177e-4f98-a814-8321d48ac3f8" + "uuid": "98296574-945c-4fb7-836c-9c909d2e83f4" } ] }, - "9": { + "8": { "annotation": "", "content_id": null, "errors": null, - "id": 9, + "id": 8, "input_connections": {}, "inputs": [ { @@ -472,7 +438,7 @@ "outputs": [], "position": { "left": 869.9487341129009, - "top": 1754.5394012044476 + "top": 1420.5809298273402 }, "tool_id": null, "tool_state": "{\"default\": \"CCCTAA\", \"parameter_type\": \"text\", \"optional\": true}", @@ -484,15 +450,15 @@ { "label": null, "output_name": "output", - "uuid": "5e5257ba-9346-40cc-9bba-ac680f94d9b7" + "uuid": "1692d5ed-c93b-47bc-978a-c36a43f67e67" } ] }, - 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"id": 41, + "id": 36, "input_connections": { "input": { - "id": 38, + "id": 32, "output_name": "outFileName" }, "pretext": { - "id": 39, + "id": 35, "output_name": "pretext_map_out" } }, @@ -2100,7 +1902,7 @@ ], "position": { "left": 3269.5178835851193, - "top": 1374.6872264059493 + "top": 1040.728755028842 }, "post_job_actions": { "HideDatasetActiongraph_out": { @@ -2123,18 +1925,18 @@ "when": null, "workflow_outputs": [] }, - "42": { + "37": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0", "errors": null, - "id": 42, + "id": 37, "input_connections": { "input": { - "id": 40, + "id": 34, "output_name": "out_file1" }, "pretext": { - "id": 41, + "id": 36, "output_name": "graph_out" } }, @@ -2149,7 +1951,7 @@ ], "position": { "left": 3510.9765191577903, - "top": 1200.6736037891133 + "top": 866.7151324120058 }, "post_job_actions": { "HideDatasetActiongraph_out": { @@ -2172,18 +1974,18 @@ "when": null, "workflow_outputs": [] }, - "43": { + "38": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_graph/pretext_graph/0.0.7+galaxy0", "errors": null, - "id": 43, + "id": 38, "input_connections": { "input": { - "id": 35, + "id": 30, "output_name": "out_file1" }, "pretext": { - "id": 42, + "id": 37, "output_name": "graph_out" } }, @@ -2198,7 +2000,7 @@ ], "position": { "left": 3738.4296145686367, - "top": 1034.5600763492953 + "top": 700.6016049721878 }, "post_job_actions": { "RenameDatasetActiongraph_out": { @@ -2236,14 +2038,14 @@ } ] }, - "44": { + "39": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, - "id": 44, + "id": 39, "input_connections": { "input": { - "id": 43, + "id": 38, "output_name": "graph_out" } }, @@ -2258,7 +2060,7 @@ ], "position": { "left": 4067.1634808980048, - "top": 1333.7444951512161 + "top": 999.7860237741087 }, "post_job_actions": { "RenameDatasetActionpretext_snap_out": { @@ -2298,6 +2100,6 @@ } }, "tags": [], - "uuid": "5c513816-f9d6-46f8-87e7-8701001f20ae", - "version": 26 + "uuid": "b3144383-690d-4d2b-869c-5bd1c03102c9", + "version": 27 } \ No newline at end of file From 0cf305a0f8d4450b5e147fb2f5f95f1c5bb49db4 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 20 Nov 2024 11:31:25 -0500 Subject: [PATCH 09/27] Rename folder --- .../{Curation-TreeValGal => Pre-Curation_PretextMap}/CHANGELOG.md | 0 .../PretextMap_Generation.ga | 0 .../{Curation-TreeValGal => Pre-Curation_PretextMap}/README.md | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename workflows/VGP-assembly-v2/{Curation-TreeValGal => Pre-Curation_PretextMap}/CHANGELOG.md (100%) rename workflows/VGP-assembly-v2/{Curation-TreeValGal => Pre-Curation_PretextMap}/PretextMap_Generation.ga (100%) rename workflows/VGP-assembly-v2/{Curation-TreeValGal => Pre-Curation_PretextMap}/README.md (100%) diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/CHANGELOG.md similarity index 100% rename from workflows/VGP-assembly-v2/Curation-TreeValGal/CHANGELOG.md rename to workflows/VGP-assembly-v2/Pre-Curation_PretextMap/CHANGELOG.md diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga similarity index 100% rename from workflows/VGP-assembly-v2/Curation-TreeValGal/PretextMap_Generation.ga rename to workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga diff --git a/workflows/VGP-assembly-v2/Curation-TreeValGal/README.md b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md similarity index 100% rename from workflows/VGP-assembly-v2/Curation-TreeValGal/README.md rename to workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md From 2a0c7bb72981ac188459ecca04a8378c3378afe0 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 20 Nov 2024 11:35:52 -0500 Subject: [PATCH 10/27] add release number and remove parameter from the READMA --- .../PretextMap_Generation.ga | 45 +++---------------- .../Pre-Curation_PretextMap/README.md | 15 +++---- 2 files changed, 12 insertions(+), 48 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga index 9fee03f1f..6883a8181 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga @@ -176,6 +176,7 @@ ], "format-version": "0.1", "license": "MIT", + "release": "1.0", "name": "PretextMap Generation from 2 haplotypes", "report": { "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" @@ -1015,16 +1016,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - }, - { - "description": "runtime parameter for tool Cutadapt", - "name": "library" - } - ], + "inputs": [], "label": "Trim HiC reads", "name": "Cutadapt", "outputs": [ @@ -1373,16 +1365,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Map with minimap2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool Map with minimap2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "Map with minimap2", "outputs": [ @@ -1431,16 +1414,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool BWA-MEM2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool BWA-MEM2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -1489,16 +1463,7 @@ "output_name": "out_file1" } }, - "inputs": [ - { - "description": "runtime parameter for tool BWA-MEM2", - "name": "fastq_input" - }, - { - "description": "runtime parameter for tool BWA-MEM2", - "name": "reference_source" - } - ], + "inputs": [], "label": null, "name": "BWA-MEM2", "outputs": [ diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md index bb432cfff..2160e706b 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md @@ -8,14 +8,13 @@ This workflow generates Hi-C contact maps for diploid genome assemblies in the P 1. **Haplotype 1** [fasta] 2. **Haplotype 2** [fasta] 3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information. -4. **Are the fasta files compressed?** Select `yes` if the assembly files have the format [fasta.gz] -5. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. -6. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. -7. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads -8. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads -9. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". -10. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. -11. **PacBio reads collection** [fastq] Collection of PacBio reads. +4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. +5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. +6. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads +7. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads +8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". +9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. +10. **PacBio reads collection** [fastq] Collection of PacBio reads. ## Outputs From 4de0fbc76433b9c2be30cca05814557303ae4972 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 20 Nov 2024 11:51:12 -0500 Subject: [PATCH 11/27] expose output to be used for Jbrowse2 workflow --- .../PretextMap_Generation.ga | 210 ++++++++---------- 1 file changed, 94 insertions(+), 116 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga index 6883a8181..1da8baf0c 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga @@ -4,80 +4,73 @@ "comments": [ { "child_steps": [ - 10, - 11, - 15, - 16, - 19, - 20, - 22 + 36, + 37, + 38 ], - "color": "blue", + "color": "orange", "data": { - "title": "Merge Haplotypes" + "title": "Add tracks to the Hi-C map" }, - "id": 0, + "id": 6, "position": [ - 354.6656953811405, - 1.9843677882680026 + 3160.811282791104, + 625.284367788268 ], "size": [ - 1283, - 769 + 861.8, + 613.8 ], "type": "frame" }, { "child_steps": [ - 12, - 13, - 17, - 18, - 21, - 23, - 24 + 14, + 27, + 32 ], - "color": "yellow", + "color": "green", "data": { - "title": "Optionnal: Trim Hi-C reads" + "title": "Coverage" }, - "id": 1, + "id": 5, "position": [ - 986.4656953811406, - 818.4843677882681 + 2169.511282791104, + 1456.784367788268 ], "size": [ - 1168.5, - 515.8 + 833.6, + 266.8 ], "type": "frame" }, { "child_steps": [ - 30, - 25 + 26, + 34, + 31 ], - "color": "turquoise", + "color": "lime", "data": { - "title": "Gaps" + "title": "Telomeres" }, - "id": 2, + "id": 4, "position": [ - 2125.611282791104, - 33.284367788268014 + 2314.611282791104, + 1092.184367788268 ], "size": [ - 541.9, - 212.5 + 761, + 296 ], "type": "frame" }, { "child_steps": [ - 35, 33, 28, - 29 + 29, + 35 ], "color": "red", "data": { @@ -96,64 +89,71 @@ }, { "child_steps": [ - 26, - 34, - 31 + 25, + 30 ], - "color": "lime", + "color": "turquoise", "data": { - "title": "Telomeres" + "title": "Gaps" }, - "id": 4, + "id": 2, "position": [ - 2314.611282791104, - 1092.184367788268 + 2125.611282791104, + 33.284367788268014 ], "size": [ - 761, - 296 + 541.9, + 212.5 ], "type": "frame" }, { "child_steps": [ - 32, - 14, - 27 + 12, + 13, + 17, + 18, + 21, + 23, + 24 ], - "color": "green", + "color": "yellow", "data": { - "title": "Coverage" + "title": "Optionnal: Trim Hi-C reads" }, - "id": 5, + "id": 1, "position": [ - 2169.511282791104, - 1456.784367788268 + 986.4656953811406, + 818.4843677882681 ], "size": [ - 833.6, - 266.8 + 1168.5, + 515.8 ], "type": "frame" }, { "child_steps": [ - 36, - 37, - 38 + 10, + 11, + 15, + 16, + 19, + 20, + 22 ], - "color": "orange", + "color": "blue", "data": { - "title": "Add tracks to the Hi-C map" + "title": "Merge Haplotypes" }, - "id": 6, + "id": 0, "position": [ - 3160.811282791104, - 625.284367788268 + 354.6656953811405, + 1.9843677882680026 ], "size": [ - 861.8, - 613.8 + 1283, + 769 ], "type": "frame" } @@ -199,7 +199,7 @@ "outputs": [], "position": { "left": 0, - "top": 0.0 + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", @@ -261,13 +261,7 @@ "type": "parameter_input", "uuid": "742c987a-a4b8-4208-918a-cfb4bd55cd66", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "22587979-c564-4ef6-90a6-eb9d008b1708" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "Suffix added to scaffolds belonging to haplotype 1. ", @@ -294,13 +288,7 @@ "type": "parameter_input", "uuid": "f61b5666-fa76-4892-9b1d-d31979bc5a44", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "7e0e37f8-6afe-4823-b126-b67121a87ae7" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "Suffix added to contigs belonging to haplotype 2. ", @@ -327,13 +315,7 @@ "type": "parameter_input", "uuid": "294ab686-1b84-4a79-aa5c-10553af61911", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0addc4b7-8523-44a1-b35c-b83b3914ed63" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "", @@ -414,13 +396,7 @@ "type": "parameter_input", "uuid": "6d1391db-7fef-4b5c-a236-26016d6d0aab", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "98296574-945c-4fb7-836c-9c909d2e83f4" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "", @@ -447,13 +423,7 @@ "type": "parameter_input", "uuid": "84c91e14-1709-4602-8771-eea1dadf471b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "1692d5ed-c93b-47bc-978a-c36a43f67e67" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -1073,15 +1043,15 @@ "uuid": "294dba11-0139-4167-b760-6d96683a6b68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Trimmed Hi-C reverse reads", - "output_name": "out2", - "uuid": "a3fc6dee-14d1-4524-8fff-85f4fdbc8acb" - }, { "label": "Trimmed Hi-C forward reads", "output_name": "out1", "uuid": "b1edf6cc-8ecc-40ed-9378-f0f591deb942" + }, + { + "label": "Trimmed Hi-C reverse reads", + "output_name": "out2", + "uuid": "a3fc6dee-14d1-4524-8fff-85f4fdbc8acb" } ] }, @@ -1273,9 +1243,11 @@ "action_type": "ChangeDatatypeAction", "output_name": "stats" }, - "HideDatasetActionstats": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "TagDatasetActionstats": { + "action_arguments": { + "tags": "Gaps_bed" + }, + "action_type": "TagDatasetAction", "output_name": "stats" } }, @@ -1291,7 +1263,13 @@ "type": "tool", "uuid": "7ef0994f-1ebf-4d9d-8799-cd6f42cb0c0c", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "Gaps Bed", + "output_name": "stats", + "uuid": "4a7f2ef2-c635-4ddb-b23b-8546f9290ef9" + } + ] }, "26": { "annotation": "", @@ -2065,6 +2043,6 @@ } }, "tags": [], - "uuid": "b3144383-690d-4d2b-869c-5bd1c03102c9", - "version": 27 + "uuid": "189adf80-b290-4b24-ab53-d7aca1bb75a2", + "version": 28 } \ No newline at end of file From 3cf74abb25d9a42d7cdd25efd8bbb0beae4077fd Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 25 Nov 2024 21:33:29 -0500 Subject: [PATCH 12/27] add tests --- .../Pre-Curation_PretextMap/.dockstore.yml | 28 +++++++ .../PretextMap_Generation-tests.yml | 84 +++++++++++++++++++ .../PretextMap_Generation.ga | 78 ++++++++--------- 3 files changed, 151 insertions(+), 39 deletions(-) create mode 100644 workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml create mode 100644 workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml new file mode 100644 index 000000000..0ec9e770f --- /dev/null +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml @@ -0,0 +1,28 @@ +version: 1.2 +workflows: +- name: PretextMap_Generation + subclass: Galaxy + publish: true + primaryDescriptorPath: /PretextMap_Generation.ga + testParameterFiles: + - /PretextMap_Generation-tests.yml + authors: + - name: Patrik Smeds + orcid: 0000-0001-6228-2785 + - name: Galaxy + - name: Delphine Lariviere + orcid: 0000-0001-6421-3484 +- name: Bam-To-Excel-Reads:-13-24 + subclass: Galaxy + publish: true + primaryDescriptorPath: /Bam-To-Excel-Reads:-13-24.ga +- name: PretextMap-Generation-from-2-haplotypes + subclass: Galaxy + publish: true + primaryDescriptorPath: /PretextMap-Generation-from-2-haplotypes.ga + authors: + - name: Patrik Smeds + orcid: 0000-0001-6228-2785 + - name: Galaxy + - name: Delphine Lariviere + orcid: 0000-0001-6421-3484 diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml new file mode 100644 index 000000000..281ee3d3c --- /dev/null +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml @@ -0,0 +1,84 @@ +- doc: Test outline for PretextMap-Generation-from-2-haplotypes + job: + Haplotype 1: + class: File + location: https://zenodo.org/records/14218240/files/Haplotype%201.fasta + filetype: fasta + Haplotype 2: + class: File + location: https://zenodo.org/records/14218240/files/Haplotype%202.fasta + filetype: fasta + HiC reads - forward: + class: Collection + collection_type: list + elements: + - class: File + identifier: HiC forward reads + location: https://zenodo.org/records/14218240/files/Hi-C%20forward%20reads.fastqsanger.gz + HiC reads - reverse: + class: Collection + collection_type: list + elements: + - class: File + identifier: HI-C reverse reads + location: https://zenodo.org/records/14218240/files/HI-C%20reverse%20reads.fastqsanger.gz + PacBio reads collection: + class: Collection + collection_type: list + elements: + - class: File + identifier: PacBio reads.fastq.gz + location: https://zenodo.org/records/14218240/files/PacBio%20reads%20collection.fastq.gz + Do you want to add suffixes to the scaffold names?: true + Haplotype 1 suffix: hap1 + Haplotype 2 suffix: hap2 + Do you want to trim the Hi-C data?: true + Telomere repeat to suit species: CCCTAA + outputs: + Merged haplotypes: + asserts: + has_text: + text: ">scaffold_10.hap1" + has_text: + text: ">scaffold_10.hap2" + Gaps Bed: + asserts: + has_text: + text: "scaffold_1.hap1 4100376 4100576" + has_text: + text: "scaffold_10.hap2 137138839 137139039" + seqtk-telo: + has_text: + text: "scaffold_10.hap2 0 11012 139653677" + Gaps Bedgraph: + has_text: + text: "scaffold_10.hap2 137138839 137139039 200" + BigWig coverage: + asserts: + has_size: + value : 820000 + delta: 5000 + Telomeres Bedgraph: + has_text: + text: "scaffold_10.hap2 0 11012 11012" + Trimmed Hi-C forward reads: + asserts: + has_size: + value : 143000000 + delta: 1000000 + Trimmed Hi-C reverse reads: + asserts: + has_size: + value : 148000000 + delta: 1000000 + Merged HiC alignments: + asserts: + has_size: + value : 71000000 + delta: 3000000 + graph_cov_telo_gaps: + asserts: + has_size: + value : 3000000 + delta: 1000000 + diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga index 1da8baf0c..3c93bdb91 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga @@ -47,8 +47,8 @@ { "child_steps": [ 26, - 34, - 31 + 31, + 34 ], "color": "lime", "data": { @@ -67,9 +67,34 @@ }, { "child_steps": [ - 33, + 10, + 11, + 15, + 16, + 19, + 20, + 22 + ], + "color": "blue", + "data": { + "title": "Merge Haplotypes" + }, + "id": 0, + "position": [ + 354.6656953811405, + 1.9843677882680026 + ], + "size": [ + 1283, + 769 + ], + "type": "frame" + }, + { + "child_steps": [ 28, 29, + 33, 35 ], "color": "red", @@ -131,37 +156,12 @@ 515.8 ], "type": "frame" - }, - { - "child_steps": [ - 10, - 11, - 15, - 16, - 19, - 20, - 22 - ], - "color": "blue", - "data": { - "title": "Merge Haplotypes" - }, - "id": 0, - "position": [ - 354.6656953811405, - 1.9843677882680026 - ], - "size": [ - 1283, - 769 - ], - "type": "frame" } ], "creator": [ { "class": "Person", - "identifier": "0000-0001-6228-2785", + "identifier": "https://orcid.org/0000-0001-6228-2785", "name": "Patrik Smeds" }, { @@ -170,7 +170,7 @@ }, { "class": "Person", - "identifier": "0000-0001-6421-3484", + "identifier": "https://orcid.org/0000-0001-6421-3484", "name": "Delphine Lariviere" } ], @@ -1043,15 +1043,15 @@ "uuid": "294dba11-0139-4167-b760-6d96683a6b68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Trimmed Hi-C forward reads", - "output_name": "out1", - "uuid": "b1edf6cc-8ecc-40ed-9378-f0f591deb942" - }, { "label": "Trimmed Hi-C reverse reads", "output_name": "out2", "uuid": "a3fc6dee-14d1-4524-8fff-85f4fdbc8acb" + }, + { + "label": "Trimmed Hi-C forward reads", + "output_name": "out1", + "uuid": "b1edf6cc-8ecc-40ed-9378-f0f591deb942" } ] }, @@ -1322,9 +1322,9 @@ "when": null, "workflow_outputs": [ { - "label": "default", + "label": "seqtk-telo", "output_name": "default", - "uuid": "7c340220-c54b-4b54-8b80-f5571dc73951" + "uuid": "768cd8bd-018e-413e-bdef-cac14e86d5b6" } ] }, @@ -2043,6 +2043,6 @@ } }, "tags": [], - "uuid": "189adf80-b290-4b24-ab53-d7aca1bb75a2", - "version": 28 + "uuid": "ac376ea3-f861-48b8-859c-ed1f8d4fec9a", + "version": 29 } \ No newline at end of file From 95bd01c63f1d2e507d4cf5fd0a8c8855932cae5d Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 25 Nov 2024 21:39:41 -0500 Subject: [PATCH 13/27] replace dockstore file after cleaning my local repository --- .../Pre-Curation_PretextMap/.dockstore.yml | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml index 0ec9e770f..6dec05492 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml @@ -1,6 +1,6 @@ version: 1.2 workflows: -- name: PretextMap_Generation +- name: main subclass: Galaxy publish: true primaryDescriptorPath: /PretextMap_Generation.ga @@ -12,17 +12,3 @@ workflows: - name: Galaxy - name: Delphine Lariviere orcid: 0000-0001-6421-3484 -- name: Bam-To-Excel-Reads:-13-24 - subclass: Galaxy - publish: true - primaryDescriptorPath: /Bam-To-Excel-Reads:-13-24.ga -- name: PretextMap-Generation-from-2-haplotypes - subclass: Galaxy - publish: true - primaryDescriptorPath: /PretextMap-Generation-from-2-haplotypes.ga - authors: - - name: Patrik Smeds - orcid: 0000-0001-6228-2785 - - name: Galaxy - - name: Delphine Lariviere - orcid: 0000-0001-6421-3484 From 2779664526cfc87f03f0e1ea5310d66a0be3dadd Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 26 Nov 2024 08:55:22 -0500 Subject: [PATCH 14/27] add Marius comments --- .../Pre-Curation_PretextMap/.dockstore.yml | 1 - .../PretextMap_Generation-tests.yml | 17 +- .../PretextMap_Generation.ga | 210 +++++++++--------- 3 files changed, 113 insertions(+), 115 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml index 6dec05492..64b8d2b8b 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml @@ -9,6 +9,5 @@ workflows: authors: - name: Patrik Smeds orcid: 0000-0001-6228-2785 - - name: Galaxy - name: Delphine Lariviere orcid: 0000-0001-6421-3484 diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml index 281ee3d3c..630e3dc65 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml @@ -35,7 +35,7 @@ Do you want to trim the Hi-C data?: true Telomere repeat to suit species: CCCTAA outputs: - Merged haplotypes: + Merged Haplotypes: asserts: has_text: text: ">scaffold_10.hap1" @@ -47,36 +47,39 @@ text: "scaffold_1.hap1 4100376 4100576" has_text: text: "scaffold_10.hap2 137138839 137139039" - seqtk-telo: + Seqtk-telo Output: + asserts: has_text: text: "scaffold_10.hap2 0 11012 139653677" Gaps Bedgraph: + asserts: has_text: text: "scaffold_10.hap2 137138839 137139039 200" - BigWig coverage: + BigWig Coverage: asserts: has_size: value : 820000 delta: 5000 Telomeres Bedgraph: + asserts: has_text: text: "scaffold_10.hap2 0 11012 11012" - Trimmed Hi-C forward reads: + Trimmed Hi-C Forward Reads: asserts: has_size: value : 143000000 delta: 1000000 - Trimmed Hi-C reverse reads: + Trimmed Hi-C Reverse Reads: asserts: has_size: value : 148000000 delta: 1000000 - Merged HiC alignments: + Merged HiC Alignments: asserts: has_size: value : 71000000 delta: 3000000 - graph_cov_telo_gaps: + Pretext All tracks: asserts: has_size: value : 3000000 diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga index 3c93bdb91..1bd410050 100644 --- a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga @@ -1,92 +1,74 @@ { "a_galaxy_workflow": "true", - "annotation": "", + "annotation": "This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies. ", "comments": [ { "child_steps": [ - 36, - 37, - 38 - ], - "color": "orange", - "data": { - "title": "Add tracks to the Hi-C map" - }, - "id": 6, - "position": [ - 3160.811282791104, - 625.284367788268 - ], - "size": [ - 861.8, - 613.8 - ], - "type": "frame" - }, - { - "child_steps": [ - 14, - 27, - 32 + 10, + 11, + 15, + 16, + 19, + 20, + 22 ], - "color": "green", + "color": "blue", "data": { - "title": "Coverage" + "title": "Merge Haplotypes" }, - "id": 5, + "id": 0, "position": [ - 2169.511282791104, - 1456.784367788268 + 354.6656953811405, + 1.9843677882680026 ], "size": [ - 833.6, - 266.8 + 1283, + 769 ], "type": "frame" }, { "child_steps": [ - 26, - 31, - 34 + 12, + 13, + 17, + 18, + 21, + 23, + 24 ], - "color": "lime", + "color": "yellow", "data": { - "title": "Telomeres" + "title": "Optionnal: Trim Hi-C reads" }, - "id": 4, + "id": 1, "position": [ - 2314.611282791104, - 1092.184367788268 + 986.4656953811406, + 818.4843677882681 ], "size": [ - 761, - 296 + 1168.5, + 515.8 ], "type": "frame" }, { "child_steps": [ - 10, - 11, - 15, - 16, - 19, - 20, - 22 + 25, + 30 ], - "color": "blue", + "color": "turquoise", "data": { - "title": "Merge Haplotypes" + "title": "Gaps" }, - "id": 0, + "id": 2, "position": [ - 354.6656953811405, - 1.9843677882680026 + 2125.611282791104, + 33.284367788268014 ], "size": [ - 1283, - 769 + 541.9, + 212.5 ], "type": "frame" }, @@ -114,46 +96,64 @@ }, { "child_steps": [ - 25, - 30 + 26, + 34, + 31 ], - "color": "turquoise", + "color": "lime", "data": { - "title": "Gaps" + "title": "Telomeres" }, - "id": 2, + "id": 4, "position": [ - 2125.611282791104, - 33.284367788268014 + 2314.611282791104, + 1092.184367788268 ], "size": [ - 541.9, - 212.5 + 761, + 296 ], "type": "frame" }, { "child_steps": [ - 12, - 13, - 17, - 18, - 21, - 23, - 24 + 14, + 27, + 32 ], - "color": "yellow", + "color": "green", "data": { - "title": "Optionnal: Trim Hi-C reads" + "title": "Coverage" }, - "id": 1, + "id": 5, "position": [ - 986.4656953811406, - 818.4843677882681 + 2169.511282791104, + 1456.784367788268 ], "size": [ - 1168.5, - 515.8 + 833.6, + 266.8 + ], + "type": "frame" + }, + { + "child_steps": [ + 36, + 37, + 38 + ], + "color": "orange", + "data": { + "title": "Add tracks to the Hi-C map" + }, + "id": 6, + "position": [ + 3160.811282791104, + 625.284367788268 + ], + "size": [ + 861.8, + 613.8 ], "type": "frame" } @@ -164,10 +164,6 @@ "identifier": "https://orcid.org/0000-0001-6228-2785", "name": "Patrik Smeds" }, - { - "class": "Organization", - "name": "Galaxy" - }, { "class": "Person", "identifier": "https://orcid.org/0000-0001-6421-3484", @@ -1010,14 +1006,14 @@ "post_job_actions": { "RenameDatasetActionout1": { "action_arguments": { - "newname": "Trimmed Hi-C forward reads" + "newname": "Trimmed Hi-C Forward Reads" }, "action_type": "RenameDatasetAction", "output_name": "out1" }, "RenameDatasetActionout2": { "action_arguments": { - "newname": "Trimmed Hi-C reverse reads" + "newname": "Trimmed Hi-C Reverse Reads" }, "action_type": "RenameDatasetAction", "output_name": "out2" @@ -1044,14 +1040,14 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "Trimmed Hi-C reverse reads", - "output_name": "out2", - "uuid": "a3fc6dee-14d1-4524-8fff-85f4fdbc8acb" + "label": "Trimmed Hi-C Forward Reads", + "output_name": "out1", + "uuid": "65ce5f95-c7a7-4e65-a67c-4728661c36ab" }, { - "label": "Trimmed Hi-C forward reads", - "output_name": "out1", - "uuid": "b1edf6cc-8ecc-40ed-9378-f0f591deb942" + "label": "Trimmed Hi-C Reverse Reads", + "output_name": "out2", + "uuid": "0b43d9f2-9d02-44a7-9be3-d032bee8b859" } ] }, @@ -1086,7 +1082,7 @@ "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { - "newname": "Merged haplotypes" + "newname": "Merged Haplotypes" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" @@ -1107,9 +1103,9 @@ "when": null, "workflow_outputs": [ { - "label": "Merged haplotypes", + "label": "Merged Haplotypes", "output_name": "out_file1", - "uuid": "45f8224e-8ef6-494e-bd12-bd5f292eb5cf" + "uuid": "882714cc-1c3e-4b07-bffc-c10c8c03bb81" } ] }, @@ -1302,7 +1298,7 @@ "post_job_actions": { "RenameDatasetActiondefault": { "action_arguments": { - "newname": "seqtk-telo" + "newname": "Seqtk-telo Output" }, "action_type": "RenameDatasetAction", "output_name": "default" @@ -1322,9 +1318,9 @@ "when": null, "workflow_outputs": [ { - "label": "seqtk-telo", + "label": "Seqtk-telo Output", "output_name": "default", - "uuid": "768cd8bd-018e-413e-bdef-cac14e86d5b6" + "uuid": "f63116e6-d670-441f-ba9d-4b91f2fcfa2b" } ] }, @@ -1602,7 +1598,7 @@ "post_job_actions": { "RenameDatasetActionoutFileName": { "action_arguments": { - "newname": "BigWig coverage" + "newname": "BigWig Coverage" }, "action_type": "RenameDatasetAction", "output_name": "outFileName" @@ -1629,9 +1625,9 @@ "when": null, "workflow_outputs": [ { - "label": "BigWig coverage", + "label": "BigWig Coverage", "output_name": "outFileName", - "uuid": "2d1dde5f-ee79-4a09-8576-8a47b304bfb0" + "uuid": "99e50ff7-22ae-4afc-af83-e81b69c73931" } ] }, @@ -1666,7 +1662,7 @@ "post_job_actions": { "RenameDatasetActionoutfile": { "action_arguments": { - "newname": "Merged HiC alignments" + "newname": "Merged HiC Alignments" }, "action_type": "RenameDatasetAction", "output_name": "outfile" @@ -1693,9 +1689,9 @@ "when": null, "workflow_outputs": [ { - "label": "Merged HiC alignments", + "label": "Merged HiC Alignments", "output_name": "outfile", - "uuid": "1de91b04-adbb-49d3-ac19-c5c9937e17de" + "uuid": "a343390e-8d7b-45b7-8f5a-9a5fc3bbda0b" } ] }, @@ -1975,9 +1971,9 @@ "when": null, "workflow_outputs": [ { - "label": "graph_cov_telo_gaps", + "label": "Pretext All tracks", "output_name": "graph_out", - "uuid": "08120e26-6656-48a6-9b92-5c801249eb19" + "uuid": "453f5d3d-549e-4d17-88b0-444a31c43d1a" } ] }, @@ -2043,6 +2039,6 @@ } }, "tags": [], - "uuid": "ac376ea3-f861-48b8-859c-ed1f8d4fec9a", - "version": 29 + "uuid": "c2187c4e-095c-4f6b-996d-ee16204bda34", + "version": 7 } \ No newline at end of file From d4ba83e1656f83d890d3d029c212f75498446767 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 26 Nov 2024 08:57:42 -0500 Subject: [PATCH 15/27] rename folder --- .../.dockstore.yml | 0 .../CHANGELOG.md | 0 .../PretextMap_Generation-tests.yml | 0 .../PretextMap_Generation.ga | 0 .../README.md | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename workflows/VGP-assembly-v2/{Pre-Curation_PretextMap => Pre-curation-Hi-C-map-generation}/.dockstore.yml (100%) rename workflows/VGP-assembly-v2/{Pre-Curation_PretextMap => Pre-curation-Hi-C-map-generation}/CHANGELOG.md (100%) rename workflows/VGP-assembly-v2/{Pre-Curation_PretextMap => Pre-curation-Hi-C-map-generation}/PretextMap_Generation-tests.yml (100%) rename workflows/VGP-assembly-v2/{Pre-Curation_PretextMap => Pre-curation-Hi-C-map-generation}/PretextMap_Generation.ga (100%) rename workflows/VGP-assembly-v2/{Pre-Curation_PretextMap => Pre-curation-Hi-C-map-generation}/README.md (100%) diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/.dockstore.yml similarity index 100% rename from workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml rename to workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/.dockstore.yml diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/CHANGELOG.md b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/CHANGELOG.md similarity index 100% rename from workflows/VGP-assembly-v2/Pre-Curation_PretextMap/CHANGELOG.md rename to workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/CHANGELOG.md diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml similarity index 100% rename from workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation-tests.yml rename to workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga similarity index 100% rename from workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga rename to workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga diff --git a/workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md similarity index 100% rename from workflows/VGP-assembly-v2/Pre-Curation_PretextMap/README.md rename to workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md From ce121ebb22c0070ecd4602e7f6dda5f5aea92df4 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 26 Nov 2024 09:51:06 -0500 Subject: [PATCH 16/27] Make more clear that HiC reads need to be in collections --- .../PretextMap_Generation-tests.yml | 4 ++-- .../PretextMap_Generation.ga | 8 ++++---- .../Pre-curation-Hi-C-map-generation/README.md | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml index 630e3dc65..fc69a70ce 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml @@ -8,14 +8,14 @@ class: File location: https://zenodo.org/records/14218240/files/Haplotype%202.fasta filetype: fasta - HiC reads - forward: + Collection of HiC reads - forward: class: Collection collection_type: list elements: - class: File identifier: HiC forward reads location: https://zenodo.org/records/14218240/files/Hi-C%20forward%20reads.fastqsanger.gz - HiC reads - reverse: + Collection of HiC reads - reverse: class: Collection collection_type: list elements: diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index 1bd410050..bf4b04d23 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -322,10 +322,10 @@ "inputs": [ { "description": "", - "name": "HiC reads - forward" + "name": "Collection of HiC reads - forward" } ], - "label": "HiC reads - forward", + "label": "Collection of HiC reads - forward", "name": "Input dataset collection", "outputs": [], "position": { @@ -349,10 +349,10 @@ "inputs": [ { "description": "", - "name": "HiC reads - reverse" + "name": "Collection of HiC reads - reverse" } ], - "label": "HiC reads - reverse", + "label": "Collection of HiC reads - reverse", "name": "Input dataset collection", "outputs": [], "position": { diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md index 2160e706b..2a708cb2a 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md @@ -10,8 +10,8 @@ This workflow generates Hi-C contact maps for diploid genome assemblies in the P 3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information. 4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. 5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. -6. **HiC reads - forward** [fastq] Collection containing the Hi-C forward reads -7. **HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads +6. **Collection of HiC reads - forward** [fastq] Collection containing the Hi-C forward reads +7. **Collection of HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads 8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". 9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. 10. **PacBio reads collection** [fastq] Collection of PacBio reads. From a8fc19fd4fccc4bf31c5d8a5fd7d2d93d9920d98 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 26 Nov 2024 11:49:05 -0500 Subject: [PATCH 17/27] use smaller test data --- .../PretextMap_Generation-tests.yml | 42 +++++++++---------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml index fc69a70ce..4d6e98c14 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml @@ -2,11 +2,11 @@ job: Haplotype 1: class: File - location: https://zenodo.org/records/14218240/files/Haplotype%201.fasta + location: https://zenodo.org/records/14224931/files/Haplotype%201.fasta filetype: fasta Haplotype 2: class: File - location: https://zenodo.org/records/14218240/files/Haplotype%202.fasta + location: https://zenodo.org/records/14224931/files/Haplotype%202.fasta filetype: fasta Collection of HiC reads - forward: class: Collection @@ -14,21 +14,21 @@ elements: - class: File identifier: HiC forward reads - location: https://zenodo.org/records/14218240/files/Hi-C%20forward%20reads.fastqsanger.gz + location: https://zenodo.org/records/14224931/files/HiC%20forward.fastqsanger.gz Collection of HiC reads - reverse: class: Collection collection_type: list elements: - class: File identifier: HI-C reverse reads - location: https://zenodo.org/records/14218240/files/HI-C%20reverse%20reads.fastqsanger.gz + location: https://zenodo.org/records/14224931/files/HiC%20reverse.fastqsanger.gz PacBio reads collection: class: Collection collection_type: list elements: - class: File identifier: PacBio reads.fastq.gz - location: https://zenodo.org/records/14218240/files/PacBio%20reads%20collection.fastq.gz + location: https://zenodo.org/records/14224931/files/PacBio%20reads.fastq.gz Do you want to add suffixes to the scaffold names?: true Haplotype 1 suffix: hap1 Haplotype 2 suffix: hap2 @@ -38,50 +38,50 @@ Merged Haplotypes: asserts: has_text: - text: ">scaffold_10.hap1" + text: ">scaffold_1.hap1" has_text: - text: ">scaffold_10.hap2" + text: ">scaffold_1.hap2" Gaps Bed: asserts: has_text: text: "scaffold_1.hap1 4100376 4100576" has_text: - text: "scaffold_10.hap2 137138839 137139039" + text: "scaffold_1.hap2 222907212 222907412" Seqtk-telo Output: asserts: has_text: - text: "scaffold_10.hap2 0 11012 139653677" + text: "scaffold_1.hap2 0 8505 223155965" Gaps Bedgraph: asserts: has_text: - text: "scaffold_10.hap2 137138839 137139039 200" + text: "scaffold_1.hap2 222907212 222907412 200" BigWig Coverage: asserts: has_size: - value : 820000 - delta: 5000 + value : 97000 + delta: 3000 Telomeres Bedgraph: asserts: has_text: - text: "scaffold_10.hap2 0 11012 11012" + text: "scaffold_1.hap2 0 8505 8505" Trimmed Hi-C Forward Reads: asserts: has_size: - value : 143000000 - delta: 1000000 + value : 13000000 + delta: 2000000 Trimmed Hi-C Reverse Reads: asserts: has_size: - value : 148000000 - delta: 1000000 + value : 14000000 + delta: 2000000 Merged HiC Alignments: asserts: has_size: - value : 71000000 - delta: 3000000 + value : 3000000 + delta: 1000000 Pretext All tracks: asserts: has_size: - value : 3000000 - delta: 1000000 + value : 855000 + delta: 20000 From c4611add7051b77eebf23a57bb50bfa1b384f262 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Nov 2024 09:20:15 -0500 Subject: [PATCH 18/27] Remove unnecessary specification that the input is a collection --- .../PretextMap_Generation-tests.yml | 4 ++-- .../PretextMap_Generation.ga | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml index 4d6e98c14..db52107bf 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml @@ -8,14 +8,14 @@ class: File location: https://zenodo.org/records/14224931/files/Haplotype%202.fasta filetype: fasta - Collection of HiC reads - forward: + HiC reads - forward: class: Collection collection_type: list elements: - class: File identifier: HiC forward reads location: https://zenodo.org/records/14224931/files/HiC%20forward.fastqsanger.gz - Collection of HiC reads - reverse: + HiC reads - reverse: class: Collection collection_type: list elements: diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index bf4b04d23..1bd410050 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -322,10 +322,10 @@ "inputs": [ { "description": "", - "name": "Collection of HiC reads - forward" + "name": "HiC reads - forward" } ], - "label": "Collection of HiC reads - forward", + "label": "HiC reads - forward", "name": "Input dataset collection", "outputs": [], "position": { @@ -349,10 +349,10 @@ "inputs": [ { "description": "", - "name": "Collection of HiC reads - reverse" + "name": "HiC reads - reverse" } ], - "label": "Collection of HiC reads - reverse", + "label": "HiC reads - reverse", "name": "Input dataset collection", "outputs": [], "position": { From 1ff2cd800138422ee42445118ba3c95bd79058d4 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Nov 2024 10:27:27 -0500 Subject: [PATCH 19/27] add marius comments and more details about the inputs --- .../PretextMap_Generation-tests.yml | 36 +++++----- .../PretextMap_Generation.ga | 68 +++++++++---------- .../README.md | 8 +-- 3 files changed, 56 insertions(+), 56 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml index db52107bf..e3f36563c 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml @@ -8,21 +8,21 @@ class: File location: https://zenodo.org/records/14224931/files/Haplotype%202.fasta filetype: fasta - HiC reads - forward: + Hi-C reads - forward: class: Collection collection_type: list elements: - class: File identifier: HiC forward reads location: https://zenodo.org/records/14224931/files/HiC%20forward.fastqsanger.gz - HiC reads - reverse: + Hi-C reads - reverse: class: Collection collection_type: list elements: - class: File identifier: HI-C reverse reads location: https://zenodo.org/records/14224931/files/HiC%20reverse.fastqsanger.gz - PacBio reads collection: + PacBio reads: class: Collection collection_type: list elements: @@ -38,50 +38,50 @@ Merged Haplotypes: asserts: has_text: - text: ">scaffold_1.hap1" + text: ">scaffold_10.hap1" has_text: - text: ">scaffold_1.hap2" + text: ">scaffold_10.hap2" Gaps Bed: asserts: has_text: - text: "scaffold_1.hap1 4100376 4100576" + text: "scaffold_10.hap1 34145604 34145804" has_text: - text: "scaffold_1.hap2 222907212 222907412" + text: "scaffold_10.hap2 137138839 137139039" Seqtk-telo Output: asserts: has_text: - text: "scaffold_1.hap2 0 8505 223155965" + text: "scaffold_10.hap2 0 11012 139653677" Gaps Bedgraph: asserts: has_text: - text: "scaffold_1.hap2 222907212 222907412 200" + text: "scaffold_10.hap2 137138839 137139039 200" BigWig Coverage: asserts: has_size: - value : 97000 - delta: 3000 + value : 112000 + delta: 4000 Telomeres Bedgraph: asserts: has_text: - text: "scaffold_1.hap2 0 8505 8505" + text: "scaffold_10.hap2 0 11012 11012" Trimmed Hi-C Forward Reads: asserts: has_size: - value : 13000000 + value : 13900000 delta: 2000000 Trimmed Hi-C Reverse Reads: asserts: has_size: - value : 14000000 + value : 14300000 delta: 2000000 - Merged HiC Alignments: + Merged Hi-C Alignments: asserts: has_size: - value : 3000000 + value : 4600000 delta: 1000000 Pretext All tracks: asserts: has_size: - value : 855000 - delta: 20000 + value : 946900 + delta: 40000 diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index 1bd410050..bd25d1d68 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies. ", + "annotation": "This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.", "comments": [ { "child_steps": [ @@ -179,14 +179,14 @@ }, "steps": { "0": { - "annotation": "fasta file for haplotype 1", + "annotation": "Assembly for Haplotype 1.", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "fasta file for haplotype 1", + "description": "Assembly for Haplotype 1.", "name": "Haplotype 1" } ], @@ -206,14 +206,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "fasta file for haplotype 2\n", + "annotation": "Assembly for Haplotype 2.", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "fasta file for haplotype 2\n", + "description": "Assembly for Haplotype 2.", "name": "Haplotype 2" } ], @@ -233,14 +233,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", + "annotation": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1). Necessary if the assemblies don't already have a marker of haplotype in the scaffold names. ", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1).", + "description": "Add haplotype suffix to the scaffold names (e.g. Scaffold_1_hap1). Necessary if the assemblies don't already have a marker of haplotype in the scaffold names. ", "name": "Do you want to add suffixes to the scaffold names?" } ], @@ -260,14 +260,14 @@ "workflow_outputs": [] }, "3": { - "annotation": "Suffix added to scaffolds belonging to haplotype 1. ", + "annotation": "Suffix added to scaffolds belonging to haplotype 1.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Suffix added to scaffolds belonging to haplotype 1. ", + "description": "Suffix added to scaffolds belonging to haplotype 1.", "name": "Haplotype 1 suffix" } ], @@ -287,14 +287,14 @@ "workflow_outputs": [] }, "4": { - "annotation": "Suffix added to contigs belonging to haplotype 2. ", + "annotation": "Suffix added to contigs belonging to haplotype 2.", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "Suffix added to contigs belonging to haplotype 2. ", + "description": "Suffix added to contigs belonging to haplotype 2.", "name": "Haplotype 2 suffix" } ], @@ -322,10 +322,10 @@ "inputs": [ { "description": "", - "name": "HiC reads - forward" + "name": "Hi-C reads - forward" } ], - "label": "HiC reads - forward", + "label": "Hi-C reads - forward", "name": "Input dataset collection", "outputs": [], "position": { @@ -349,15 +349,15 @@ "inputs": [ { "description": "", - "name": "HiC reads - reverse" + "name": "Hi-C reads - reverse" } ], - "label": "HiC reads - reverse", + "label": "Hi-C reads - reverse", "name": "Input dataset collection", "outputs": [], "position": { - "left": 665.0496572173611, - "top": 1166.1304399701626 + "left": 665.0468622199531, + "top": 1166.693055524258 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -368,14 +368,14 @@ "workflow_outputs": [] }, "7": { - "annotation": "Trim 5 bases at the end of the paired reads. Use with some Arima hiC if the Hi-C map looks \"noisy\".", + "annotation": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\".", "content_id": null, "errors": null, "id": 7, "input_connections": {}, "inputs": [ { - "description": "Trim 5 bases at the end of the paired reads. Use with some Arima hiC if the Hi-C map looks \"noisy\".", + "description": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\".", "name": "Do you want to trim the Hi-C data?" } ], @@ -395,14 +395,14 @@ "workflow_outputs": [] }, "8": { - "annotation": "", + "annotation": "The default value is set for vertebrate genomes (CCCTAA).", "content_id": null, "errors": null, "id": 8, "input_connections": {}, "inputs": [ { - "description": "", + "description": "The default value is set for vertebrate genomes (CCCTAA).", "name": "Telomere repeat to suit species" } ], @@ -430,10 +430,10 @@ "inputs": [ { "description": "", - "name": "PacBio reads collection" + "name": "PacBio reads" } ], - "label": "PacBio reads collection", + "label": "PacBio reads", "name": "Input dataset collection", "outputs": [], "position": { @@ -983,7 +983,7 @@ } }, "inputs": [], - "label": "Trim HiC reads", + "label": "Trim Hi-C reads", "name": "Cutadapt", "outputs": [ { @@ -1039,15 +1039,15 @@ "uuid": "294dba11-0139-4167-b760-6d96683a6b68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Trimmed Hi-C Forward Reads", - "output_name": "out1", - "uuid": "65ce5f95-c7a7-4e65-a67c-4728661c36ab" - }, { "label": "Trimmed Hi-C Reverse Reads", "output_name": "out2", "uuid": "0b43d9f2-9d02-44a7-9be3-d032bee8b859" + }, + { + "label": "Trimmed Hi-C Forward Reads", + "output_name": "out1", + "uuid": "65ce5f95-c7a7-4e65-a67c-4728661c36ab" } ] }, @@ -1662,7 +1662,7 @@ "post_job_actions": { "RenameDatasetActionoutfile": { "action_arguments": { - "newname": "Merged HiC Alignments" + "newname": "Merged Hi-C Alignments" }, "action_type": "RenameDatasetAction", "output_name": "outfile" @@ -1689,9 +1689,9 @@ "when": null, "workflow_outputs": [ { - "label": "Merged HiC Alignments", + "label": "Merged Hi-C Alignments", "output_name": "outfile", - "uuid": "a343390e-8d7b-45b7-8f5a-9a5fc3bbda0b" + "uuid": "95cf9c54-17a5-4000-b632-06f4a5d15730" } ] }, @@ -2039,6 +2039,6 @@ } }, "tags": [], - "uuid": "c2187c4e-095c-4f6b-996d-ee16204bda34", - "version": 7 + "uuid": "723f6ab9-53dd-4156-afe1-0d7e63963b71", + "version": 14 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md index 2a708cb2a..9cd9a33b1 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md @@ -10,11 +10,11 @@ This workflow generates Hi-C contact maps for diploid genome assemblies in the P 3. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information. 4. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names. 5. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names. -6. **Collection of HiC reads - forward** [fastq] Collection containing the Hi-C forward reads -7. **Collection of HiC reads - reverse** [fastq] Collection containing the Hi-C reverse reads -8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with some Arima Hi-C if the Hi-C map looks "noisy". +6. **Hi-C reads - forward** [fastq] Collection containing the Hi-C forward reads +7. **Hi-C reads - reverse** [fastq] Collection containing the Hi-C reverse reads +8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with Arima Hi-C data if the Hi-C map looks "noisy". 9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates. -10. **PacBio reads collection** [fastq] Collection of PacBio reads. +10. **PacBio reads** [fastq] Collection of PacBio reads. ## Outputs From 306265e0f9c16ada86040a165aaaac554c1b1f6a Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Nov 2024 11:44:48 -0500 Subject: [PATCH 20/27] correct typo --- .../Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index bd25d1d68..645644d15 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -39,7 +39,7 @@ ], "color": "yellow", "data": { - "title": "Optionnal: Trim Hi-C reads" + "title": "Optional: Trim Hi-C reads" }, "id": 1, "position": [ From 47076324256578bf82b8fdccde7426fdf7d866ac Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Nov 2024 11:45:06 -0500 Subject: [PATCH 21/27] use even smaller data --- .../PretextMap_Generation-tests.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml index e3f36563c..1c5563576 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml @@ -2,11 +2,11 @@ job: Haplotype 1: class: File - location: https://zenodo.org/records/14224931/files/Haplotype%201.fasta + location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta filetype: fasta Haplotype 2: class: File - location: https://zenodo.org/records/14224931/files/Haplotype%202.fasta + location: https://zenodo.org/records/14230702/files/Haplotype%202.fasta filetype: fasta Hi-C reads - forward: class: Collection @@ -14,21 +14,21 @@ elements: - class: File identifier: HiC forward reads - location: https://zenodo.org/records/14224931/files/HiC%20forward.fastqsanger.gz + location: https://zenodo.org/records/14230702/files/HiC%20forward.fastqsanger.gz Hi-C reads - reverse: class: Collection collection_type: list elements: - class: File identifier: HI-C reverse reads - location: https://zenodo.org/records/14224931/files/HiC%20reverse.fastqsanger.gz + location: https://zenodo.org/records/14230702/files/HiC%20reverse.fastqsanger.gz PacBio reads: class: Collection collection_type: list elements: - class: File identifier: PacBio reads.fastq.gz - location: https://zenodo.org/records/14224931/files/PacBio%20reads.fastq.gz + location: https://zenodo.org/records/14230702/files/PacBio%20reads.fastq.gz Do you want to add suffixes to the scaffold names?: true Haplotype 1 suffix: hap1 Haplotype 2 suffix: hap2 From 14c03d2619898e69a8d81523064ba905f93f154a Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 27 Nov 2024 13:41:59 -0500 Subject: [PATCH 22/27] rename output of Gfastats --- .../PretextMap_Generation.ga | 99 ++++++++++--------- 1 file changed, 53 insertions(+), 46 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index 645644d15..7e0b317f6 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -4,26 +4,42 @@ "comments": [ { "child_steps": [ - 10, - 11, - 15, - 16, - 19, - 20, - 22 + 37, + 38, + 36 ], - "color": "blue", + "color": "orange", "data": { - "title": "Merge Haplotypes" + "title": "Add tracks to the Hi-C map" }, - "id": 0, + "id": 6, "position": [ - 354.6656953811405, - 1.9843677882680026 + 3160.811282791104, + 625.284367788268 ], "size": [ - 1283, - 769 + 861.8, + 613.8 + ], + "type": "frame" + }, + { + "child_steps": [ + 25, + 30 + ], + "color": "turquoise", + "data": { + "title": "Gaps" + }, + "id": 2, + "position": [ + 2125.611282791104, + 33.284367788268014 + ], + "size": [ + 541.9, + 212.5 ], "type": "frame" }, @@ -54,21 +70,26 @@ }, { "child_steps": [ - 25, - 30 + 10, + 11, + 15, + 16, + 19, + 20, + 22 ], - "color": "turquoise", + "color": "blue", "data": { - "title": "Gaps" + "title": "Merge Haplotypes" }, - "id": 2, + "id": 0, "position": [ - 2125.611282791104, - 33.284367788268014 + 354.6656953811405, + 1.9843677882680026 ], "size": [ - 541.9, - 212.5 + 1283, + 769 ], "type": "frame" }, @@ -135,27 +156,6 @@ 266.8 ], "type": "frame" - }, - { - "child_steps": [ - 36, - 37, - 38 - ], - "color": "orange", - "data": { - "title": "Add tracks to the Hi-C map" - }, - "id": 6, - "position": [ - 3160.811282791104, - 625.284367788268 - ], - "size": [ - 861.8, - 613.8 - ], - "type": "frame" } ], "creator": [ @@ -1239,6 +1239,13 @@ "action_type": "ChangeDatatypeAction", "output_name": "stats" }, + "RenameDatasetActionstats": { + "action_arguments": { + "newname": "Gaps Bed" + }, + "action_type": "RenameDatasetAction", + "output_name": "stats" + }, "TagDatasetActionstats": { "action_arguments": { "tags": "Gaps_bed" @@ -2039,6 +2046,6 @@ } }, "tags": [], - "uuid": "723f6ab9-53dd-4156-afe1-0d7e63963b71", - "version": 14 + "uuid": "eebaa808-859f-4ac7-b103-2fb3043ec99e", + "version": 1 } \ No newline at end of file From 425d64c53e0c295fbc5b2a961d49463c89909189 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Fri, 13 Dec 2024 08:35:36 -0500 Subject: [PATCH 23/27] update tools --- .../PretextMap_Generation.ga | 184 +++++++++--------- 1 file changed, 92 insertions(+), 92 deletions(-) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga index 7e0b317f6..509a5a24a 100644 --- a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga +++ b/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga @@ -4,67 +4,86 @@ "comments": [ { "child_steps": [ - 37, - 38, - 36 + 28, + 29, + 33, + 35 ], - "color": "orange", + "color": "red", "data": { - "title": "Add tracks to the Hi-C map" + "title": "Generate Hi-C map" }, - "id": 6, + "id": 3, "position": [ - 3160.811282791104, - 625.284367788268 + 2296.411282791104, + 492.684367788268 ], "size": [ - 861.8, - 613.8 + 779.6, + 512.7 ], "type": "frame" }, { "child_steps": [ - 25, - 30 + 31, + 26, + 34 ], - "color": "turquoise", + "color": "lime", "data": { - "title": "Gaps" + "title": "Telomeres" }, - "id": 2, + "id": 4, "position": [ - 2125.611282791104, - 33.284367788268014 + 2314.611282791104, + 1092.184367788268 ], "size": [ - 541.9, - 212.5 + 761, + 296 ], "type": "frame" }, { "child_steps": [ - 12, - 13, - 17, - 18, - 21, - 23, - 24 + 14, + 27, + 32 ], - "color": "yellow", + "color": "green", "data": { - "title": "Optional: Trim Hi-C reads" + "title": "Coverage" }, - "id": 1, + "id": 5, "position": [ - 986.4656953811406, - 818.4843677882681 + 2169.511282791104, + 1456.784367788268 ], "size": [ - 1168.5, - 515.8 + 833.6, + 266.8 + ], + "type": "frame" + }, + { + "child_steps": [ + 36, + 37, + 38 + ], + "color": "orange", + "data": { + "title": "Add tracks to the Hi-C map" + }, + "id": 6, + "position": [ + 3160.811282791104, + 625.284367788268 + ], + "size": [ + 861.8, + 613.8 ], "type": "frame" }, @@ -95,65 +114,46 @@ }, { "child_steps": [ - 28, - 29, - 33, - 35 - ], - "color": "red", - "data": { - "title": "Generate Hi-C map" - }, - "id": 3, - "position": [ - 2296.411282791104, - 492.684367788268 - ], - "size": [ - 779.6, - 512.7 - ], - "type": "frame" - }, - { - "child_steps": [ - 26, - 34, - 31 + 12, + 13, + 17, + 18, + 21, + 23, + 24 ], - "color": "lime", + "color": "yellow", "data": { - "title": "Telomeres" + "title": "Optional: Trim Hi-C reads" }, - "id": 4, + "id": 1, "position": [ - 2314.611282791104, - 1092.184367788268 + 986.4656953811406, + 818.4843677882681 ], "size": [ - 761, - 296 + 1168.5, + 515.8 ], "type": "frame" }, { "child_steps": [ - 14, - 27, - 32 + 25, + 30 ], - "color": "green", + "color": "turquoise", "data": { - "title": "Coverage" + "title": "Gaps" }, - "id": 5, + "id": 2, "position": [ - 2169.511282791104, - 1456.784367788268 + 2125.611282791104, + 33.284367788268014 ], "size": [ - 833.6, - 266.8 + 541.9, + 212.5 ], "type": "frame" } @@ -698,8 +698,8 @@ } ], "position": { - "left": 786.2749522007948, - "top": 94.63563858285602 + "left": 786.2655911487304, + "top": 93.76611659335607 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1209,7 +1209,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "errors": null, "id": 25, "input_connections": { @@ -1254,15 +1254,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "764f2516d837", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"coordinates\", \"__current_case__\": 1, \"out_coord\": \"g\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"coordinates\", \"__current_case__\": 1, \"out_coord\": \"g\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.9+galaxy1", "type": "tool", "uuid": "7ef0994f-1ebf-4d9d-8799-cd6f42cb0c0c", "when": null, @@ -1640,7 +1640,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, "id": 33, "input_connections": { @@ -1682,15 +1682,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "tool_shed_repository": { - "changeset_revision": "25ca5d73aedf", + "changeset_revision": "321347bd0494", "name": "bellerophon", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"forward\": {\"__class__\": \"ConnectedValue\"}, \"quality\": \"0\", \"reverse\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0+galaxy0", + "tool_version": "1.0+galaxy1", "type": "tool", "uuid": "4bfdb10c-5477-4105-9a82-1ca064d27f12", "when": null, @@ -1986,7 +1986,7 @@ }, "39": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0", "errors": null, "id": 39, "input_connections": { @@ -2024,15 +2024,15 @@ "output_name": "pretext_snap_out" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "44c66e8d21e6", + "changeset_revision": "26f2fe7e53a1", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__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}", - "tool_version": "0.0.3+galaxy1", + "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}", + "tool_version": "0.0.4+galaxy0", "type": "tool", "uuid": "533b33d8-3a3b-480a-9978-1526d65606c5", "when": null, @@ -2046,6 +2046,6 @@ } }, "tags": [], - "uuid": "eebaa808-859f-4ac7-b103-2fb3043ec99e", + "uuid": "455f372b-0e81-4297-b98c-39cb1b3822bf", "version": 1 } \ No newline at end of file From db8b8ad1838d30f1e035c7eba6aaeaa8771d3da1 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 16 Dec 2024 15:32:40 -0500 Subject: [PATCH 24/27] renaming folder with more descriptive name --- .../.dockstore.yml | 0 .../CHANGELOG.md | 0 .../README.md | 0 .../hi-c-map-for-assembly-manual-curation-tests.yml} | 0 .../hi-c-map-for-assembly-manual-curation.ga} | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename workflows/VGP-assembly-v2/{Pre-curation-Hi-C-map-generation => Hi-C-contact-map-for-assembly-manual-curation}/.dockstore.yml (100%) rename workflows/VGP-assembly-v2/{Pre-curation-Hi-C-map-generation => Hi-C-contact-map-for-assembly-manual-curation}/CHANGELOG.md (100%) rename workflows/VGP-assembly-v2/{Pre-curation-Hi-C-map-generation => Hi-C-contact-map-for-assembly-manual-curation}/README.md (100%) rename workflows/VGP-assembly-v2/{Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml => Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml} (100%) rename workflows/VGP-assembly-v2/{Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga => Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga} (100%) diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/.dockstore.yml b/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/.dockstore.yml similarity index 100% rename from workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/.dockstore.yml rename to workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/.dockstore.yml diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/CHANGELOG.md b/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/CHANGELOG.md similarity index 100% rename from workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/CHANGELOG.md rename to workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/CHANGELOG.md diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md b/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/README.md similarity index 100% rename from workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/README.md rename to workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/README.md diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml b/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml similarity index 100% rename from workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml rename to workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml diff --git a/workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga b/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga similarity index 100% rename from workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation.ga rename to workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga From 67f1492bc49f4a05c777e123472505ac8cf6fcc8 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 16 Dec 2024 15:35:14 -0500 Subject: [PATCH 25/27] change folder name to lower case --- .../.dockstore.yml | 0 .../CHANGELOG.md | 0 .../README.md | 0 .../hi-c-map-for-assembly-manual-curation-tests.yml | 0 .../hi-c-map-for-assembly-manual-curation.ga | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename workflows/VGP-assembly-v2/{Hi-C-contact-map-for-assembly-manual-curation => hi-c-contact-map-for-assembly-manual-curation}/.dockstore.yml (100%) rename workflows/VGP-assembly-v2/{Hi-C-contact-map-for-assembly-manual-curation => hi-c-contact-map-for-assembly-manual-curation}/CHANGELOG.md (100%) rename workflows/VGP-assembly-v2/{Hi-C-contact-map-for-assembly-manual-curation => hi-c-contact-map-for-assembly-manual-curation}/README.md (100%) rename workflows/VGP-assembly-v2/{Hi-C-contact-map-for-assembly-manual-curation => hi-c-contact-map-for-assembly-manual-curation}/hi-c-map-for-assembly-manual-curation-tests.yml (100%) rename workflows/VGP-assembly-v2/{Hi-C-contact-map-for-assembly-manual-curation => hi-c-contact-map-for-assembly-manual-curation}/hi-c-map-for-assembly-manual-curation.ga (100%) diff --git a/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/.dockstore.yml b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml similarity index 100% rename from workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/.dockstore.yml rename to workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml diff --git a/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/CHANGELOG.md b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md similarity index 100% rename from workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/CHANGELOG.md rename to workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md diff --git a/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/README.md b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md similarity index 100% rename from workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/README.md rename to workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md diff --git a/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml similarity index 100% rename from workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml rename to workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml diff --git a/workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga similarity index 100% rename from workflows/VGP-assembly-v2/Hi-C-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga rename to workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga From 0911819664e5b728a0975c642f38869611ac4701 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 16 Dec 2024 15:40:20 -0500 Subject: [PATCH 26/27] Improve name of the Workflow --- .../hi-c-contact-map-for-assembly-manual-curation/README.md | 2 +- .../hi-c-map-for-assembly-manual-curation-tests.yml | 2 +- .../hi-c-map-for-assembly-manual-curation.ga | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md index 9cd9a33b1..8299d3076 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md @@ -1,4 +1,4 @@ -# PretextMap generation +# Hi-C Contact map generation for manual curation of genome assemblies : 2 haplotypes This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies. diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml index 1c5563576..c21eed056 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml @@ -1,4 +1,4 @@ -- doc: Test outline for PretextMap-Generation-from-2-haplotypes +- doc: Test outline for hi-c-map-for-assembly-manual-curation.ga job: Haplotype 1: class: File diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga index 509a5a24a..de0da9bdf 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga @@ -173,7 +173,7 @@ "format-version": "0.1", "license": "MIT", "release": "1.0", - "name": "PretextMap Generation from 2 haplotypes", + "name": "Hi-C Contact map generation for manual curation of genome assemblies : 2 haplotypes", "report": { "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" }, From 3264afa53192f6e365ba0c69324cf39648d4aebf Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Mon, 16 Dec 2024 15:54:21 -0500 Subject: [PATCH 27/27] update dockstore file --- .../.dockstore.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml index 64b8d2b8b..669ef8da4 100644 --- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml +++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml @@ -3,9 +3,9 @@ workflows: - name: main subclass: Galaxy publish: true - primaryDescriptorPath: /PretextMap_Generation.ga + primaryDescriptorPath: /hi-c-map-for-assembly-manual-curation.ga testParameterFiles: - - /PretextMap_Generation-tests.yml + - /hi-c-map-for-assembly-manual-curation-tests.yml authors: - name: Patrik Smeds orcid: 0000-0001-6228-2785