diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga index 4e2cbc5994..ab6230db82 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "BSD-3-Clause", - "release": "0.3", + "release": "0.4", "name": "Assembly-decontamination-VGP9", "report": { "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -64,7 +64,7 @@ "top": 692.7734375 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "4bd1b150-bdb0-4458-9ddc-62bc29356aa2", @@ -124,7 +124,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0", "errors": null, "id": 3, "input_connections": { @@ -160,15 +160,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0", "tool_shed_repository": { - "changeset_revision": "86755160afbf", + "changeset_revision": "3dc70b59608c", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.5+galaxy0", "type": "tool", "uuid": "5089350b-c1a9-498a-9786-9864d484f77a", "when": null, @@ -448,7 +448,7 @@ } }, "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.2", "type": "tool", "uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016", @@ -457,7 +457,7 @@ }, "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0", "errors": null, "id": 10, "input_connections": { @@ -486,15 +486,15 @@ "top": 423.9453125 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0", "tool_shed_repository": { - "changeset_revision": "86755160afbf", + "changeset_revision": "3dc70b59608c", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", + "tool_version": "9.5+galaxy0", "type": "tool", "uuid": "5b7e33a0-0ec4-4539-bb91-0c862597df69", "when": null, @@ -508,7 +508,7 @@ }, "11": { "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/1.3.10+galaxy0", "errors": null, "id": 11, "input_connections": { @@ -535,15 +535,15 @@ "top": 798.078125 }, "post_job_actions": {}, - "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/1.3.10+galaxy0", "tool_shed_repository": { - "changeset_revision": "3ef480892a9f", + "changeset_revision": "50b6ec4074f4", "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.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3.6+galaxy0", + "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3.10+galaxy0", "type": "tool", "uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed", "when": null, @@ -561,4 +561,4 @@ ], "uuid": "aa4960d9-198d-4990-a393-a98efcd3070a", "version": 3 -} \ No newline at end of file +} diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md index 4b36ae76b7..df95f21bdc 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.4] 2025-03-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.10+galaxy0` + ## [0.3] - 2024-08-26 - Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes. diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/README.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/README.md new file mode 100644 index 0000000000..4082e0c949 --- /dev/null +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/README.md @@ -0,0 +1,14 @@ +## Decontamination Workflow + +Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite. + +### Inputs + +- Genome Assembly [fasta] +- Database for Kraken2. Database containing the possible contaminants. + +### Ouput + +- List of contaminant scaffolds +- List of mitochondrial scaffolds +- Decontaminated assembly