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 1ef065c98..3e6d55a61 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 @@ -10,18 +10,18 @@ ], "format-version": "0.1", "license": "BSD-3-Clause", - "release": "0.1", - "name": "VGP Decontamination pipeline - Db not included", + "release":"0.1", + "name": "Assembly-decontamination-VGP9", "steps": { "0": { - "annotation": "(s2 for VGP genomes) ", + "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "(s2 for VGP genomes) ", + "description": "", "name": "Scaffolded assembly (fasta)" } ], @@ -30,142 +30,75 @@ "outputs": [], "position": { "left": 0, - "top": 534.25 + "top": 431.99609375 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "8ad5c808-6c7e-4f18-b12c-3becae89e23d", + "uuid": "f3335a9f-1793-4ba2-98d8-253eb5380a3f", + "when": null, "workflow_outputs": [] }, "1": { - "annotation": "We recommend using the database: PlusPF - Standard ", + "annotation": "Select the database to query to identify non-target contaminants.", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "We recommend using the database: PlusPF - Standard ", - "name": "Kraken 2 Database" + "description": "Select the database to query to identify non-target contaminants.", + "name": "Database for Kraken2" } ], - "label": "Kraken 2 Database", + "label": "Database for Kraken2", "name": "Input parameter", "outputs": [], "position": { - "left": 1233, - "top": 0 + "left": 72.984375, + "top": 545.19140625 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "f416691c-2ce1-40e9-b77f-a94579b93f07", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a552f922-3a75-4838-901d-68b515f61cc8" - } - ] + "uuid": "4bd1b150-bdb0-4458-9ddc-62bc29356aa2", + "when": null, + "workflow_outputs": [] }, "2": { - "annotation": "We recommend importing the database : https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/mitochondrion.1.1.genomic.fna.gz ", + "annotation": "Select the database to query to identify mitochondrial contaminants.", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "We recommend importing the database : https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/mitochondrion.1.1.genomic.fna.gz ", - "name": "Refseq Mitochondrion Database" + "description": "Select the database to query to identify mitochondrial contaminants.", + "name": "Mitochondria Database for BLAST" } ], - "label": "Refseq Mitochondrion Database", + "label": "Mitochondria Database for BLAST", "name": "Input dataset", "outputs": [], "position": { - "left": 1259, - "top": 683 + "left": 545.00390625, + "top": 675.12109375 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "ad03817a-57d2-4859-94ba-3adcdeac2ae1", + "uuid": "162f7aed-b552-48e4-8ed9-bbf568f8e1a3", + "when": null, "workflow_outputs": [] }, "3": { - "annotation": "Data input 'include_bed' (bed)\nGenerates output on a subset list of headers or coordinates in 0-based bed format. It can be combined with --exclude-bed. Optional (--include-bed)", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "Data input 'include_bed' (bed)\nGenerates output on a subset list of headers or coordinates in 0-based bed format. It can be combined with --exclude-bed. 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Optional (--swiss-army-knife)", - "name": "SAK input file - Optional" - } - ], - "label": "SAK input file - Optional", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 2773, - "top": 861 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": \"\"}", - "tool_version": null, - "type": "data_input", - "uuid": "c0cdad27-b551-467c-a379-1a868387789c", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "7bc2de1b-387f-45a6-9e8a-d77696ce7719" - } - ] - }, - "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1", "errors": null, - "id": 5, + "id": 3, "input_connections": { "infile": { "id": 0, @@ -173,98 +106,49 @@ } }, "inputs": [], - "label": null, - "name": "Text reformatting", + "label": "lower to uppercase", + "name": "Text transformation", "outputs": [ { - "name": "outfile", + "name": "output", "type": "input" } ], "position": { - 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