diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga index 35ba3b166..6f7f236ea 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.5", + "release": "0.6", "name": "Assembly-Hifi-Trio-phasing-VGP5", "report": { "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=merqury_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -455,7 +455,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0", "errors": null, "id": 16, "input_connections": { @@ -506,15 +506,15 @@ "output_name": "out1" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "5eb7e84243f2", + "changeset_revision": "c0b2c2e39c9c", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": \"1\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}]}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"json_stats\", \"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy1", + "tool_version": "5.0+galaxy0", "type": "tool", "uuid": "b8770ddb-2ec4-4ef5-8362-6531e559554d", "when": null, @@ -1178,7 +1178,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 30, "input_connections": { @@ -1220,15 +1220,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}, \"no_sequence\": false}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "ae31efe9-7f56-4a2d-b811-d77d4f8b0abf", "when": null, @@ -1242,7 +1242,7 @@ }, "31": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 31, "input_connections": { @@ -1284,15 +1284,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"no\", \"__current_case__\": 0}, \"no_sequence\": false}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "f2a02b12-43b7-4969-a999-dbc18b820c2f", "when": null, @@ -1359,7 +1359,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 33, "input_connections": { @@ -1415,15 +1415,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "653200d3-c548-4dd2-87cb-e8b40fbc8235", "when": null, @@ -1437,7 +1437,7 @@ }, "34": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 34, "input_connections": { @@ -1493,15 +1493,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "name": "gfastats", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "77c35546-0668-45d5-aa10-2c5048fd4256", "when": null, @@ -1515,7 +1515,7 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 35, "input_connections": { @@ -1546,15 +1546,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "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\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "fb185c69-e1a1-47a4-b983-d25d94f25522", "when": null, @@ -1562,7 +1562,7 @@ }, "36": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 36, "input_connections": { @@ -1593,15 +1593,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "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\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "a3de4200-b7d2-4cd5-bcca-fa6f548ed6a0", "when": null, @@ -1609,7 +1609,7 @@ }, "37": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 37, "input_connections": { @@ -1644,15 +1644,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "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\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "60492710-1411-45ff-abe6-1c94644bcca4", "when": null, @@ -1660,7 +1660,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "errors": null, "id": 38, "input_connections": { @@ -1695,15 +1695,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2", "tool_shed_repository": { - "changeset_revision": "764f2516d837", + "changeset_revision": "7729cd89aaf7", "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\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.9+galaxy1", + "tool_version": "1.3.9+galaxy2", "type": "tool", "uuid": "904feec3-140a-4aff-a8af-29592733175e", "when": null, @@ -2467,7 +2467,7 @@ } }, "tags": [], - "uuid": "45a56829-3c02-421f-bd8e-33571a6551bb" + "uuid": "d76d11f4-06f3-4d86-abd5-39a3e065e2e3" }, "tool_id": null, "type": "subworkflow", @@ -2849,7 +2849,7 @@ } }, "tags": [], - "uuid": "31ca169e-9cb6-4e38-b356-8ced1da32bf3" + "uuid": "a248ea17-f514-4b62-a492-6f98e33d59da" }, "tool_id": null, "type": "subworkflow", @@ -3741,7 +3741,7 @@ } }, "tags": [], - "uuid": "8cc09c34-e184-4acc-bc4c-7242f362e838" + "uuid": "18ec5add-5064-496a-a9f7-161ce2b65bcb" }, "tool_id": null, "type": "subworkflow", diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md index 66a0b1e52..364ee9479 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.6] 2025-02-10 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy2` + ## [0.5] 2025-01-27 ### Automatic update