diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index 2aadf88ff..1f403a8df 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -20,7 +20,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.3", + "release": "0.2.4", "name": "Assembly-Hifi-HiC-phasing-VGP4", "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_qv\")\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\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\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" @@ -73,7 +73,7 @@ "top": 149.4296875 }, "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "46d0bd3a-f4fd-48ab-ba51-31838a288248", @@ -208,7 +208,7 @@ "top": 666.080035105452 }, "tool_id": null, - "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "245a5b51-c40d-4425-81ca-2baf3c157022", @@ -235,7 +235,7 @@ "top": 770.3740188995779 }, "tool_id": null, - "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", @@ -316,7 +316,7 @@ "top": 1033.0113085913417 }, "tool_id": null, - "tool_state": "{\"default\": 37, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", @@ -370,7 +370,7 @@ "top": 1228.4076056463502 }, "tool_id": null, - "tool_state": "{\"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "b251eddc-49e6-4899-a893-a904c29b9e75", @@ -406,7 +406,7 @@ }, "14": { "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": 14, "input_connections": { @@ -462,15 +462,15 @@ "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\": [\"report\", \"json_stats\"], \"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": "64ce3a66-9497-4937-a1b6-7f72814f1fe1", "when": null, @@ -697,7 +697,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0", "errors": null, "id": 20, "input_connections": { @@ -724,15 +724,15 @@ "top": 388 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0", "tool_shed_repository": { - "changeset_revision": "f7e2f1eb3a16", + "changeset_revision": "a7e081ceb76a", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.24.1+galaxy0", + "tool_version": "1.27+galaxy0", "type": "tool", "uuid": "c60d4342-a7fb-4dd1-8f5f-206fa7e423b8", "when": null, @@ -740,7 +740,7 @@ }, "21": { "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": 21, "input_connections": { @@ -790,15 +790,15 @@ "output_name": "out2" } }, - "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\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"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\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"5\", \"cut2\": \"5\", \"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\": null, \"read_mod_options\": {\"strip_suffix\": null, \"length_tag\": null, \"rename\": null, \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.9+galaxy1", + "tool_version": "5.0+galaxy0", "type": "tool", "uuid": "009e0075-cbca-449c-97ef-2b5d68ef5d00", "when": "$(inputs.when)", @@ -1512,7 +1512,7 @@ }, "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": { @@ -1554,15 +1554,15 @@ "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": "001f8c0e-234a-4406-9d8b-a26b8e878c56", "when": null, @@ -1570,7 +1570,7 @@ }, "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": { @@ -1612,15 +1612,15 @@ "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": "fe43bf41-0e43-482e-99bb-7a855d4bcb2f", "when": null, @@ -1628,7 +1628,7 @@ }, "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": { @@ -1666,15 +1666,15 @@ "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": "723d5c3e-c0ec-4085-bccd-29d5d97ce3f8", "when": null, @@ -1682,7 +1682,7 @@ }, "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": { @@ -1720,15 +1720,15 @@ "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__\": \"RuntimeValue\"}, \"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__\": \"RuntimeValue\"}, \"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": "4d4a30a0-d2e9-4814-afc2-74e4194ebdf5", "when": null, @@ -1742,7 +1742,7 @@ }, "39": { "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": 39, "input_connections": { @@ -1780,15 +1780,15 @@ "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": "ed95e95b-68f3-47f4-ac03-eb4fb01d3020", "when": null, @@ -1796,7 +1796,7 @@ }, "40": { "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": 40, "input_connections": { @@ -1834,15 +1834,15 @@ "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__\": \"RuntimeValue\"}, \"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__\": \"RuntimeValue\"}, \"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": "2bf6f1be-461a-45e1-aa5f-0af394563a23", "when": null, @@ -1856,7 +1856,7 @@ }, "41": { "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": 41, "input_connections": { @@ -1889,15 +1889,15 @@ "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\": \"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": "596ea56e-3c73-402a-b1ae-e2be1bb91227", "when": null, @@ -1905,7 +1905,7 @@ }, "42": { "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": 42, "input_connections": { @@ -1938,15 +1938,15 @@ "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\": \"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": "cd65bf95-931d-4514-8851-6652198c7ab7", "when": null, @@ -2416,7 +2416,7 @@ } }, "tags": [], - "uuid": "03c518f1-59f2-4f3c-95d1-fcfc538367e4" + "uuid": "77dc94d5-42d5-46d7-8cca-cc8f6d71d38e" }, "tool_id": null, "type": "subworkflow", @@ -2798,7 +2798,7 @@ } }, "tags": [], - "uuid": "f4b33e48-2c28-432c-8661-3f13c8787d77" + "uuid": "603e5b60-6891-4f89-ac82-f809e42bff29" }, "tool_id": null, "type": "subworkflow", @@ -3100,7 +3100,7 @@ "top": 296.3210144042969 }, "tool_id": null, - "tool_state": "{\"default\": \"Primary\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6118c82a-61da-4856-9e25-1f0d93297527", @@ -3133,7 +3133,7 @@ "top": 440.4403076171875 }, "tool_id": null, - "tool_state": "{\"default\": \"Alternate\", \"validators\": [], \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "3204b6e0-bd83-4a8d-8ddb-3b0dd89dbd04", @@ -3493,7 +3493,7 @@ } }, "tags": [], - "uuid": "03e9ffe6-27ec-4092-a507-75c4bf8bd30c" + "uuid": "d9762f5e-86be-4e3b-ac57-06630940a6c1" }, "tool_id": null, "type": "subworkflow", @@ -4269,4 +4269,4 @@ ], "uuid": "a4513aba-433a-46a0-84cc-f675a29b205b", "version": 4 -} \ No newline at end of file +} diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index e729a8cb5..1f4f15462 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.2.4] 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/iuc/multiqc/multiqc/1.24.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+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` + ## [0.2.3] 2025-01-13 ### Changes