Skip to content

Commit

Permalink
replace character in statistic table that was causing problems in the…
Browse files Browse the repository at this point in the history 
… report
  • Loading branch information
@Delphine-L
Delphine-L committed Jul 18, 2024
1 parent 62c4fcb commit 0f0a644
Showing 1 changed file with 92 additions and 87 deletions.
179 changes: 92 additions & 87 deletions workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
"release": "0.1.12",
"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_display(output=\"Assembly statistics for Hap1 and Hap2\")\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"
"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"
},
"steps": {
"0": {
Expand Down Expand Up @@ -186,13 +186,7 @@
"type": "parameter_input",
"uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "a7c8f776-78b1-4caa-b63f-f2cb96c9308b"
}
]
"workflow_outputs": []
},
"6": {
"annotation": "",
Expand All @@ -219,13 +213,7 @@
"type": "parameter_input",
"uuid": "41d1bb31-75f9-4034-abad-96aed4916b45",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "d130c749-1851-491e-83a2-794f3ca263a1"
}
]
"workflow_outputs": []
},
"7": {
"annotation": "",
Expand All @@ -252,13 +240,7 @@
"type": "parameter_input",
"uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "63859139-a7ef-4b30-a6a3-6b849b90d650"
}
]
"workflow_outputs": []
},
"8": {
"annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.",
Expand All @@ -285,13 +267,7 @@
"type": "parameter_input",
"uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "81580b69-a114-4351-b9ae-b64f2ecc930c"
}
]
"workflow_outputs": []
},
"9": {
"annotation": "",
Expand All @@ -318,13 +294,7 @@
"type": "data_input",
"uuid": "557a2e2b-008c-4566-836a-6509950aa85b",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "c191eaba-164b-424c-949b-a0582810d785"
}
]
"workflow_outputs": []
},
"10": {
"annotation": "If empty, read coverage will be estimated from the Genomescope parameters. ",
Expand All @@ -351,13 +321,7 @@
"type": "parameter_input",
"uuid": "b251eddc-49e6-4899-a893-a904c29b9e75",
"when": null,
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "fe00ec3a-b6cd-4b28-ac33-98fd7c119b75"
}
]
"workflow_outputs": []
},
"11": {
"annotation": "GenomeScope model parameters generated by K-mer profiling workflow",
Expand Down Expand Up @@ -1666,7 +1630,7 @@
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0.0,
"left": 0,
"top": 189.90056800842285
},
"tool_id": null,
Expand Down Expand Up @@ -1699,7 +1663,7 @@
],
"position": {
"left": 302.6136245727539,
"top": 0.0
"top": 0
},
"post_job_actions": {
"HideDatasetActionout_file1": {
Expand Down Expand Up @@ -2048,7 +2012,7 @@
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0.0,
"left": 0,
"top": 189.90056800842285
},
"tool_id": null,
Expand Down Expand Up @@ -2081,7 +2045,7 @@
],
"position": {
"left": 302.6136245727539,
"top": 0.0
"top": 0
},
"post_job_actions": {
"HideDatasetActionout_file1": {
Expand Down Expand Up @@ -2540,7 +2504,7 @@
}
},
"tool_id": "join1",
"tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"fill_empty\", \"__current_case__\": 1, \"fill_columns_by\": \"fill_unjoined_only\", \"do_fill_empty_columns\": {\"column_fill_type\": \"single_fill_value\", \"__current_case__\": 0, \"fill_value\": \".\"}}, \"header\": \"\", \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"fill_empty\", \"__current_case__\": 1, \"fill_columns_by\": \"fill_unjoined_only\", \"do_fill_empty_columns\": {\"column_fill_type\": \"single_fill_value\", \"__current_case__\": 0, \"fill_value\": \".\"}}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.1.3",
"type": "tool",
"uuid": "00e95547-9451-4c37-bc19-b29de3864c6a",
Expand Down Expand Up @@ -2620,8 +2584,8 @@
"name": "Input dataset",
"outputs": [],
"position": {
"left": 0.0,
"top": 0.0
"left": 0,
"top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
Expand Down Expand Up @@ -3078,25 +3042,15 @@
"uuid": "1b8e2d4e-3380-4414-bdb0-b356383c0ee2",
"when": null,
"workflow_outputs": [
{
"label": "Nx Plot",
"output_name": "Nx Plot",
"uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4"
},
{
"label": null,
"output_name": "3:output",
"uuid": "58904682-a049-4844-a9a9-fa3a83e67415"
},
{
"label": null,
"output_name": "2:output",
"uuid": "997a0a2c-a9f4-47b0-b096-be9f4617ec91"
},
{
"label": "Size Plot",
"output_name": "Size Plot",
"uuid": "03a0d2a8-c2d5-4ca7-80fe-7d04d1c4894a"
},
{
"label": "Nx Plot",
"output_name": "Nx Plot",
"uuid": "781f8511-c3fe-4954-afa8-d21c94c996a4"
}
]
},
Expand Down Expand Up @@ -3194,6 +3148,11 @@
"uuid": "08066bc3-0992-4606-844d-16be3c56691a",
"when": null,
"workflow_outputs": [
{
"label": "Busco Summary Image Hap2",
"output_name": "summary_image",
"uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1"
},
{
"label": "Busco Summary Hap2",
"output_name": "busco_sum",
Expand All @@ -3203,11 +3162,6 @@
"label": "Busco Gff File - Hap2",
"output_name": "busco_gff",
"uuid": "3b8e8b67-ad7d-4d30-a253-e601d3e201d2"
},
{
"label": "Busco Summary Image Hap2",
"output_name": "summary_image",
"uuid": "84725fc4-3480-44a2-abc0-abc8f54addb1"
}
]
},
Expand Down Expand Up @@ -3328,16 +3282,6 @@
"uuid": "9985e575-3113-4c2c-bc2c-78faab3a1291",
"when": null,
"workflow_outputs": [
{
"label": "Merqury QV",
"output_name": "qv_files",
"uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814"
},
{
"label": "Merqury Stats",
"output_name": "stats_files",
"uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3"
},
{
"label": "Merqury images",
"output_name": "png_files",
Expand All @@ -3347,6 +3291,16 @@
"label": "Merqury Histograms",
"output_name": "hist_files",
"uuid": "67d9d45d-989d-43c0-9ebd-0da9cc35763a"
},
{
"label": "Merqury QV",
"output_name": "qv_files",
"uuid": "5ba07c29-6ca5-42bd-a1e8-f4f6a35c3814"
},
{
"label": "Merqury Stats",
"output_name": "stats_files",
"uuid": "22a82fae-74cf-4024-9815-ba6a9892aac3"
}
]
},
Expand Down Expand Up @@ -3449,15 +3403,15 @@
"output_name": "summary_image",
"uuid": "cfac3083-4c1e-4bb4-91a5-eba5d19f2757"
},
{
"label": "Busco Summary Hap1",
"output_name": "busco_sum",
"uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8"
},
{
"label": "Busco Gff File - Hap1",
"output_name": "busco_gff",
"uuid": "ba26cb24-25d4-4669-982c-abe4816753a6"
},
{
"label": "Busco Summary Hap1",
"output_name": "busco_sum",
"uuid": "bd6443ea-5266-4dfc-8f1e-aded27317da8"
}
]
},
Expand Down Expand Up @@ -3790,12 +3744,63 @@
"uuid": "c10c5102-6b26-4cdc-bc35-50af09e36d9d"
}
]
},
"51": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"errors": null,
"id": 51,
"input_connections": {
"infile": {
"id": 44,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "Replace",
"outputs": [
{
"name": "outfile",
"type": "input"
}
],
"position": {
"left": 2973.2736415223585,
"top": 446.09145245110693
},
"post_job_actions": {
"HideDatasetActionoutfile": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "outfile"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#\", \"replace_pattern\": \"Number of\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "7528118f-3c8c-47a8-86e8-6085145c38d1",
"when": null,
"workflow_outputs": [
{
"label": "clean_stats",
"output_name": "outfile",
"uuid": "0d69a8ab-29c1-4fef-97d9-af243ca8eb83"
}
]
}
},
"tags": [
"VGP",
"Reviewed"
],
"uuid": "a128697a-2106-483f-9bbd-67b78c21b832",
"version": 24
"uuid": "4135d455-ac66-4d86-b4a3-643580ff877f",
"version": 5
}

0 comments on commit 0f0a644

Please sign in to comment.