From fc0371532169f3c91d8e91ee8a45eb51e09b0fbc Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 23 Apr 2024 14:08:03 -0400 Subject: [PATCH 1/2] Addition of outputs for merqury and busco --- .../CHANGELOG.md | 6 + .../Purging-duplicates-one-haplotype-VGP6b.ga | 468 ++++++++---------- 2 files changed, 221 insertions(+), 253 deletions(-) diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index 2b5663068..c81bf9e47 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.6] 2024-04-23 + +- Aff Merqury histogram output +- Aff Busco gff output +- Hunhide Merqury QV output + ## [0.5] 2024-04-22 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga index 157930135..db9d55c79 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.5", + "release": "0.6", "name": "Purging-duplicates-one-haplotype-VGP6b ", "steps": { "0": { @@ -35,7 +35,7 @@ "outputs": [], "position": { "left": 0, - "top": 36.02430839035473 + "top": 73.94776585535702 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -62,7 +62,7 @@ "outputs": [], "position": { "left": 558.0468791193098, - "top": 408.0208291659224 + "top": 445.9442866309247 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -89,7 +89,7 @@ "outputs": [], "position": { "left": 432.94921875, - "top": 938.5 + "top": 976.4234574650022 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}", @@ -116,7 +116,7 @@ "outputs": [], "position": { "left": 1972.4566892558003, - "top": 271.05034258817113 + "top": 308.9738000531734 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -135,21 +135,21 @@ "inputs": [ { "description": "", - "name": "Estimated genome size - Parameter File" + "name": "Assembly to leave alone (need this for merqury)" } ], - "label": "Estimated genome size - Parameter File", + "label": "Assembly to leave alone (need this for merqury)", "name": "Input dataset", "outputs": [], "position": { - "left": 1693.6113702942387, - "top": 1061.0416654868025 + "left": 1972.4566892558003, + "top": 428.92176735660996 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "f19aebb2-3ee9-44dc-ad1e-af4aada02e31", + "uuid": "86fed2c5-2b3d-4917-a376-f30d182a3967", "when": null, "workflow_outputs": [] }, @@ -162,21 +162,21 @@ "inputs": [ { "description": "", - "name": "Assembly to leave alone (need this for merqury)" + "name": "Estimated genome size - Parameter File" } ], - "label": "Assembly to leave alone (need this for merqury)", + "label": "Estimated genome size - Parameter File", "name": "Input dataset", "outputs": [], "position": { - "left": 1972.4566892558003, - "top": 390.9983098916077 + "left": 1693.6113702942387, + "top": 1098.9651229518047 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "86fed2c5-2b3d-4917-a376-f30d182a3967", + "uuid": "f19aebb2-3ee9-44dc-ad1e-af4aada02e31", "when": null, "workflow_outputs": [] }, @@ -197,7 +197,7 @@ "outputs": [], "position": { "left": 2540.373300171866, - "top": 362.02259306689524 + "top": 399.9460505318975 }, "tool_id": null, "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}", @@ -224,7 +224,7 @@ "outputs": [], "position": { "left": 2540.373300171866, - "top": 502.00524759962667 + "top": 539.928705064629 }, "tool_id": null, "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}", @@ -256,7 +256,7 @@ ], "position": { "left": 279.14929817609004, - "top": 31.006954533047733 + "top": 68.93041199805002 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -294,16 +294,7 @@ "output_name": "output" } }, - "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": [ @@ -314,7 +305,7 @@ ], "position": { "left": 836.9531477685715, - "top": 384.010453083438 + "top": 421.9339105484403 }, "post_job_actions": { "ChangeDatatypeActionalignment_output": { @@ -355,12 +346,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -371,7 +357,7 @@ ], "position": { "left": 835.7031135648554, - "top": 705.9723141493163 + "top": 743.8957716143186 }, "post_job_actions": { "HideDatasetActionsplit_fasta": { @@ -396,92 +382,92 @@ }, "11": { "annotation": "", - "content_id": "param_value_from_file", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 11, "input_connections": { - "input1": { + "input_file": { "id": 4, "output_name": "output" } }, "inputs": [], - "label": "Estimated genome size", - "name": "Parse parameter value", + "label": null, + "name": "gfastats", "outputs": [ { - "name": "integer_param", - "type": "expression.json" + "name": "stats", + "type": "tabular" } ], "position": { - "left": 1972.4566892558003, - "top": 1035.0261487504602 + "left": 2261.4845426800953, + "top": 679.8505909035362 }, "post_job_actions": { - "HideDatasetActioninteger_param": { + "HideDatasetActionstats": { "action_arguments": {}, "action_type": "HideDatasetAction", - "output_name": "integer_param" - }, - "RenameDatasetActioninteger_param": { - "action_arguments": { - "newname": "Estimated Genome size" - }, - "action_type": "RenameDatasetAction", - "output_name": "integer_param" + "output_name": "stats" } }, - "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", + "tool_shed_repository": { + "changeset_revision": "3ef480892a9f", + "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\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.6+galaxy0", "type": "tool", - 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"top": 0 + "top": 37.923457465002286 }, "post_job_actions": { "HideDatasetActioninteger_param": { @@ -1131,7 +1108,7 @@ ], "position": { "left": 836.9531477685715, - "top": 191.9791860478278 + "top": 229.90264351283008 }, "post_job_actions": { "HideDatasetActioninteger_param": { @@ -1155,7 +1132,7 @@ "id": 20, "input_connections": { "infile": { - "id": 16, + "id": 17, "output_name": "stats" } }, @@ -1170,7 +1147,7 @@ ], "position": { "left": 2540.373300171866, - "top": 1010.0260981547028 + "top": 1047.949555619705 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1212,12 +1189,7 @@ "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1248,7 +1220,7 @@ ], "position": { "left": 1125.9375626626565, - "top": 6.9618163142784795 + "top": 44.885273779280766 }, "post_job_actions": { "TagDatasetActioncalcuts_cutoff": { @@ -1338,20 +1310,7 @@ "output_name": "alignment_output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - }, - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - }, - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1366,7 +1325,7 @@ ], "position": { "left": 1414.6961876965902, - "top": 574.0018060167882 + "top": 611.9252634817906 }, "post_job_actions": { "TagDatasetActionpurge_dups_bed": { @@ -1420,7 +1379,7 @@ ], "position": { "left": 1693.6113702942387, - "top": 660.9722592757281 + "top": 698.8957167407304 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -1460,16 +1419,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - }, - { - "description": "runtime parameter for tool Purge overlaps", - "name": "function_select" - } - ], + "inputs": [], "label": null, "name": "Purge overlaps", "outputs": [ @@ -1484,7 +1434,7 @@ ], "position": { "left": 1972.4566892558003, - "top": 761.8837658237778 + "top": 799.80722328878 }, "post_job_actions": { "RenameDatasetActionget_seqs_hap": { @@ -1559,7 +1509,7 @@ "output_name": "get_seqs_purged" }, "mode|assembly_options|assembly_02": { - "id": 5, + "id": 4, "output_name": "output" }, "mode|meryldb_F1": { @@ -1567,12 +1517,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merqury", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Merqury", "outputs": [ @@ -1588,14 +1533,18 @@ "name": "stats_files", "type": "input" }, + { + "name": "hist_files", + "type": "input" + }, { "name": "log_file", "type": "txt" } ], "position": { - "left": 2254.25, - "top": 148.1914074209294 + "left": 2270.374846462181, + "top": 0.0 }, "post_job_actions": { "HideDatasetActionlog_file": { @@ -1603,11 +1552,6 @@ "action_type": "HideDatasetAction", "output_name": "log_file" }, - "HideDatasetActionqv_files": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "qv_files" - }, "TagDatasetActionbed_files": { "action_arguments": { "tags": "merqury_p_bed, #p" @@ -1615,6 +1559,13 @@ "action_type": "TagDatasetAction", "output_name": "bed_files" }, + "TagDatasetActionhist_files": { + "action_arguments": { + "tags": "merqury_purged_hist,name:purged" + }, + "action_type": "TagDatasetAction", + "output_name": "hist_files" + }, "TagDatasetActionpng_files": { "action_arguments": { "tags": "merqury_purged_png, #purged" @@ -1658,21 +1609,26 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}, \"assembly_02\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"RuntimeValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"RuntimeValue\"}, \"assembly_02\": {\"__class__\": \"RuntimeValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\", \"hist\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy4", "type": "tool", "uuid": "4c0ee7aa-643d-4583-b507-0def031e329b", "when": null, "workflow_outputs": [ + { + "label": "Merqury on Phased assemblies: Images", + "output_name": "png_files", + "uuid": "4b7c4a1c-42e6-4d63-999d-bdce891470cd" + }, { "label": "Merqury on Phased assemblies: stats", "output_name": "stats_files", "uuid": "c07cd28e-86b5-4e4f-87fa-bc2b3b65da33" }, { - "label": "Merqury on Phased assemblies: Images", - "output_name": "png_files", - "uuid": "4b7c4a1c-42e6-4d63-999d-bdce891470cd" + "label": "qv_files", + "output_name": "qv_files", + "uuid": "9fb50959-0da7-4838-9f0e-9c945f04c1f6" } ] }, @@ -1698,7 +1654,7 @@ ], "position": { "left": 2267.44140625, - "top": 815.45703125 + "top": 853.3804887150022 }, "post_job_actions": { "HideDatasetActionstats": { @@ -1758,13 +1714,24 @@ { "name": "summary_image", "type": "png" + }, + { + "name": "busco_gff", + "type": "gff3" } ], "position": { - "left": 2271.07421875, - "top": 1169.796875 + "left": 2265.9340461481925, + "top": 1160.1390956326313 }, "post_job_actions": { + "TagDatasetActionbusco_gff": { + "action_arguments": { + "tags": "busco_purged_gff,name:purged" + }, + "action_type": "TagDatasetAction", + "output_name": "busco_gff" + }, "TagDatasetActionbusco_missing": { "action_arguments": { "tags": "busco_purged_missing, #purged" @@ -1801,7 +1768,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"vertebrata_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"vertebrata_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "5.5.0+galaxy0", "type": "tool", "uuid": "73b62ef3-0002-418e-9f10-22076c1e48f3", @@ -1828,32 +1795,35 @@ "input_file": { "id": 24, "output_name": "get_seqs_purged" - }, - "mode_condition|statistics_condition|expected_genomesize": { - "id": 11, - "output_name": "integer_param" } }, "inputs": [], - "label": null, + "label": "Convert purged fasta to gfa", "name": "gfastats", "outputs": [ { - "name": "stats", - "type": "tabular" + "name": "output", + "type": "fastq" } ], "position": { - "left": 2261.8984375, - "top": 1687.4235851553044 + "left": 2539.288422879884, + "top": 1275.7967731581887 }, "post_job_actions": { - "TagDatasetActionstats": { + "RenameDatasetActionoutput": { "action_arguments": { - "tags": "gfastats_purged" + "newname": "Purged assembly (GFA)" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + }, + "TagDatasetActionoutput": { + "action_arguments": { + "tags": "purged_assembly_gfa" }, "action_type": "TagDatasetAction", - "output_name": "stats" + "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", @@ -1863,16 +1833,16 @@ "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\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.6+galaxy0", "type": "tool", - "uuid": "ff2b02d1-f6dc-4cd6-bd4a-a70e4d97492c", + "uuid": "90cfbc84-a100-4795-a376-f93ffe2dbd0b", "when": null, "workflow_outputs": [ { - "label": "Purged assembly statistics", - "output_name": "stats", - "uuid": "c98fd03e-3a3d-472b-8b13-f13479fc4dad" + "label": "Purged assembly (GFA)", + "output_name": "output", + "uuid": "25213685-ed44-44a7-84fd-8d92f9d1d734" } ] }, @@ -1885,40 +1855,32 @@ "input_file": { "id": 24, "output_name": "get_seqs_purged" + }, + "mode_condition|statistics_condition|expected_genomesize": { + "id": 12, + "output_name": "integer_param" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], - "label": "Convert purged fasta to gfa", + "inputs": [], + "label": null, "name": "gfastats", "outputs": [ { - "name": "output", - "type": "fastq" + "name": "stats", + "type": "tabular" } ], "position": { - "left": 2539.288422879884, - "top": 1237.8733156931864 + "left": 2267.472206693373, + "top": 1758.2151057082503 }, "post_job_actions": { - "RenameDatasetActionoutput": { - "action_arguments": { - "newname": "Purged assembly (GFA)" - }, - "action_type": "RenameDatasetAction", - "output_name": "output" - }, - "TagDatasetActionoutput": { + "TagDatasetActionstats": { "action_arguments": { - "tags": "purged_assembly_gfa" + "tags": "gfastats_purged" }, "action_type": "TagDatasetAction", - "output_name": "output" + "output_name": "stats" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", @@ -1928,16 +1890,16 @@ "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\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"1000\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3.6+galaxy0", "type": "tool", - "uuid": "90cfbc84-a100-4795-a376-f93ffe2dbd0b", + "uuid": "ff2b02d1-f6dc-4cd6-bd4a-a70e4d97492c", "when": null, "workflow_outputs": [ { - "label": "Purged assembly (GFA)", - "output_name": "output", - "uuid": "25213685-ed44-44a7-84fd-8d92f9d1d734" + "label": "Purged assembly statistics", + "output_name": "stats", + "uuid": "c98fd03e-3a3d-472b-8b13-f13479fc4dad" } ] }, @@ -1957,7 +1919,7 @@ "outputs": [], "position": { "left": 2540.373300171866, - "top": 813.0121828374843 + "top": 850.9356403024865 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2325,7 +2287,7 @@ "id": 31, "input_connections": { "infile": { - "id": 28, + "id": 29, "output_name": "stats" } }, @@ -2340,7 +2302,7 @@ ], "position": { "left": 2540.373300171866, - "top": 1596.97919245039 + "top": 1634.9026499153922 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -2368,7 +2330,7 @@ "id": 32, "input_connections": { "Alternate data": { - "id": 17, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, @@ -2394,7 +2356,7 @@ "outputs": [], "position": { "left": 2839.1842345748423, - "top": 720.9896475213042 + "top": 758.9131049863065 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2927,7 +2889,7 @@ ], "position": { "left": 2839.1842345748423, - "top": 1040.0087291593652 + "top": 1077.9321866243674 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -2962,6 +2924,6 @@ "tags": [ "VGP_curated" ], - "uuid": "8bc1fd02-cd63-4750-8856-7286a10ef14d", - "version": 15 -} + "uuid": "f069b3f3-7cf9-40f9-b452-ee9c21466623", + "version": 1 +} \ No newline at end of file From c5b7bf007aa1e34e4db0a5bc65fcc4e89611d4a6 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Mon, 29 Apr 2024 17:36:09 +0200 Subject: [PATCH 2/2] Fix the changelog --- .../Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md index c81bf9e47..f587eae87 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -2,9 +2,11 @@ ## [0.6] 2024-04-23 -- Aff Merqury histogram output -- Aff Busco gff output -- Hunhide Merqury QV output +### Changed + +- Add Merqury histogram output +- Add Busco gff output +- Unhide Merqury QV output ## [0.5] 2024-04-22