From 38ffbb1d5504a6b5e46cd775ebc61ee50bdc9726 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Thu, 29 Sep 2022 13:43:04 -0400 Subject: [PATCH 01/13] Creation of a clean branch for Hifiasm simple assembly workflow --- .../VGP-WF3-Assembly/.dockstore.yml | 7 + .../VGP-WF3-Assembly/.vscode/settings.json | 5 + .../VGP-WF3-Assembly/Assembly-(WF3)-tests.yml | 65 + .../VGP-WF3-Assembly/Assembly-(WF3).ga | 2745 +++++++++++++++++ .../Estimated Genome size.expression.json | 1 + 5 files changed, 2823 insertions(+) create mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/.dockstore.yml create mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/.vscode/settings.json create mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml create mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga create mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json diff --git 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+ "VGP", + "Reviewed" + ], + "uuid": "41efeec2-5b76-437e-a113-449139178af4", + "version": 0 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json new file mode 100644 index 000000000..3954aed74 --- /dev/null +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json @@ -0,0 +1 @@ +2288021 \ No newline at end of file From 1eec57dea68ec1056e9bee98b4a4ea263d0b31af Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 18 Sep 2023 10:27:48 +0200 Subject: [PATCH 02/13] Reduce number of workflow outputs --- .../VGP-WF3-Assembly/.vscode/settings.json | 5 - .../VGP-WF3-Assembly/Assembly-(WF3)-tests.yml | 18 +- .../VGP-WF3-Assembly/Assembly-(WF3).ga | 222 +++++------------- 3 files changed, 55 insertions(+), 190 deletions(-) delete mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/.vscode/settings.json diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/.vscode/settings.json b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/.vscode/settings.json deleted file mode 100644 index 6c2ff60b6..000000000 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/.vscode/settings.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "githubPullRequests.ignoredPullRequestBranches": [ - "master" - ] -} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml index 0215074b8..6c9cf1032 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml @@ -19,7 +19,7 @@ Name of primary assembly: Primary Name of alternate assembly: Alternate outputs: - 'MultiQC on input dataset(s): Webpage': + multiqc html report: asserts: has_size: value : 345000000 @@ -44,22 +44,8 @@ asserts: has_line: line: "# scaffolds 87" - 'Scatterplot with ggplot2 on input dataset(s): png': + Nx Plot: asserts: has_size: value : 60000 delta: 10000 - 'MultiQC on input dataset(s): Stats': - element_tests: - cutadapt: - asserts: - has_n_lines: - n: 2 - general_stats: - asserts: - has_n_lines: - n: 2 - sources: - asserts: - has_n_lines: - n: 2 \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga index b3daf80f7..78dbb8189 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga @@ -14,14 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1", - "name": "Assembly (WF3)", - "source_metadata": { - "trs_server": "dockstore", - "trs_tool_id": "#workflow/github.com/Delphine-L/iwc/WF3-Assembly", - "trs_url": "", - "trs_version_id": "VGP" - }, + "name": "Assembly (WF3) (imported from URL)", "steps": { "0": { "annotation": "", @@ -129,13 +122,7 @@ "type": "data_input", "uuid": "b7958e14-2495-4d38-8da1-ea583f5ae8e2", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2e494d29-31ee-4cab-8671-64fe3b710052" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "", @@ -162,13 +149,7 @@ "type": "parameter_input", "uuid": "163c033f-85ce-46e5-b00a-3b3904dea278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "36ffacff-2339-4901-a395-9af085cc52ef" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "", @@ -195,13 +176,7 @@ "type": "parameter_input", "uuid": "88e40054-8605-4746-b91b-38ff85c70fd6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "530227fb-66b7-47f1-8213-8bcdf9bba090" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "", @@ -252,18 +227,7 @@ "type": "tool", "uuid": "f679b5eb-cc26-4005-9499-3ad2eb4698d4", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "report", - "uuid": "f0371062-a812-4384-8e8e-3e96f7c94578" - }, - { - "label": null, - "output_name": "out1", - "uuid": "a2f2b8e1-8744-41c9-8954-d8a849f791d7" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "", @@ -335,8 +299,8 @@ } ], "position": { - "left": 811.2642211914062, - "top": 720.7812118530273 + "left": 749.6564364957525, + "top": 692.448333004384 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", @@ -353,14 +317,14 @@ "when": null, "workflow_outputs": [ { - "label": "MultiQC on input dataset(s): Webpage", - "output_name": "html_report", - "uuid": "29c25e37-c21c-4a4d-aa36-0a6e41fcfffd" + "label": "cutadapt multiqc stats", + "output_name": "stats", + "uuid": "c274f7aa-095e-4245-b6aa-cfadcf0d1736" }, { - "label": "MultiQC on input dataset(s): Stats", - "output_name": "stats", - "uuid": "0975cc13-c0b8-46a7-b21e-af99de60fe75" + "label": "multiqc html report", + "output_name": "html_report", + "uuid": "86a436db-4089-46e3-ad77-c6247302f4ce" } ] }, @@ -459,34 +423,14 @@ "when": null, "workflow_outputs": [ { - "label": null, - "output_name": "alternate_contig_graph", - "uuid": "73e06513-602f-426f-89a7-696776504290" - }, - { - "label": null, - "output_name": "noseq files", - "uuid": "6e7038ba-eedf-4795-b1fa-7dc51087b08c" - }, - { - "label": null, - "output_name": "raw_unitigs", - "uuid": "c5b0d435-da5e-45ec-959c-7b95a99fd6c5" - }, - { - "label": null, - "output_name": "log_file", - "uuid": "ebeaab1f-0c32-40aa-8818-4f64084d4b43" - }, - { - "label": null, - "output_name": "processed_unitigs", - "uuid": "70d1da67-3133-4a64-bc2f-1e1d09ac8b51" + "label": "Hifiasm Primary gfa", + "output_name": "primary_contig_graph", + "uuid": "15537a4a-9d13-48c6-9a99-42edb5a5cad0" }, { - "label": null, - "output_name": "primary_contig_graph", - "uuid": "b3e72dbf-fc80-4eed-8a59-60ef945e619b" + "label": "Hifiasm Alternate gfa", + "output_name": "alternate_contig_graph", + "uuid": "7a14aa59-72a2-4bb5-9d74-2d501577db87" } ] }, @@ -550,16 +494,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "input_file" - }, - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -569,8 +504,8 @@ } ], "position": { - "left": 2337.2584838867188, - "top": 108.70738983154297 + "left": 2276.70004629254, + "top": 108.22905619567867 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -602,7 +537,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"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\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"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": "ebb8800f-c58b-4118-93a3-a417631919db", @@ -630,16 +565,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool gfastats", - "name": "input_file" - }, - { - "description": "runtime parameter for tool gfastats", - "name": "mode_condition" - } - ], + "inputs": [], "label": null, "name": "gfastats", "outputs": [ @@ -682,7 +608,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"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\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"discover_paths\": true, \"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": "c6bd9a9c-c058-47dc-85cb-d5ba5e38490a", @@ -716,8 +642,8 @@ } ], "position": { - "left": 3043.6220703125, - "top": 667.6704330444336 + "left": 2965.1850488204186, + "top": 654.5017562211735 }, "post_job_actions": { "HideDatasetActionstats": { @@ -768,8 +694,8 @@ } ], "position": { - "left": 3042.897705078125, - "top": 808.9204330444336 + "left": 2980.283973788455, + "top": 810.3106874834958 }, "post_job_actions": { "HideDatasetActionstats": { @@ -918,24 +844,9 @@ "when": null, "workflow_outputs": [ { - "label": null, + "label": "Busco summary image", "output_name": "summary_image", - "uuid": "8a5c8cee-4cb0-49fb-befb-b15533529b6f" - }, - { - "label": null, - "output_name": "busco_sum", - "uuid": "9e000e98-8fa7-4789-8cb7-519f2b0d002b" - }, - { - "label": null, - "output_name": "busco_missing", - "uuid": "a932cb91-9075-4af3-abb1-35d017a3d797" - }, - { - "label": null, - "output_name": "busco_table", - "uuid": "980c40b4-b636-45b4-be78-9ad6a785dd55" + "uuid": "0fb12967-65f6-477f-9f68-960ca6f56f37" } ] }, @@ -1034,7 +945,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2", "tool_shed_repository": { - "changeset_revision": "f8113c25bc6b", + "changeset_revision": "589078edd230", "name": "merqury", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1046,19 +957,14 @@ "when": null, "workflow_outputs": [ { - "label": null, - "output_name": "qv_files", - "uuid": "cef0c86c-3306-4fe7-a870-2bb5a05ab7c7" + "label": "Merqury png", + "output_name": "png_files", + "uuid": "1040586b-b0aa-41c3-98e4-00ead4e43a5c" }, { - "label": null, + "label": "Merqury completeness stats", "output_name": "stats_files", - "uuid": "e61ba1b8-66e9-4e01-8fe4-46c3f0b0b156" - }, - { - "label": null, - "output_name": "png_files", - "uuid": "823f448d-7cb9-4770-a028-62d7da61f08f" + "uuid": "640107ca-7175-4624-9851-33911c197b18" } ] }, @@ -1435,13 +1341,7 @@ "type": "subworkflow", "uuid": "f7f6d8e0-74b0-479f-bb34-2f23450ffc4f", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "gfastats data for plotting", - "uuid": "5c545b4e-c7da-4661-aa73-bfe08a867cd4" - } - ] + "workflow_outputs": [] }, "19": { "annotation": "", @@ -1816,13 +1716,7 @@ "type": "subworkflow", "uuid": "be05bdc0-5016-44a9-b438-ddca2492d2d6", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "gfastats data for plotting", - "uuid": "552b85ef-4dac-432a-8f44-ce71ae933dd1" - } - ] + "workflow_outputs": [] }, "20": { "annotation": "", @@ -2399,24 +2293,14 @@ "when": null, "workflow_outputs": [ { - "label": null, - "output_name": "3:output", - "uuid": "84a0723c-c6ea-4cdf-a822-436b26b81865" - }, - { - "label": "Scatterplot with ggplot2 on input dataset(s): png", - "output_name": "Nx Plot", - "uuid": "4b4d9c80-5df1-4255-893c-81fce37e3fb3" - }, - { - "label": null, + "label": "Size Plot", "output_name": "Size Plot", - "uuid": "da997378-b1b6-4359-aee9-02494979c575" + "uuid": "e46888e6-9ae3-4310-9639-de1cdfff1871" }, { - "label": null, - "output_name": "2:output", - "uuid": "74ee96c5-3d0c-4b90-b99d-853faa8c2e04" + "label": "Nx Plot", + "output_name": "Nx Plot", + "uuid": "e34782d2-17d1-4598-92d1-93ca3d7ec7dc" } ] }, @@ -2499,8 +2383,8 @@ } ], "position": { - "left": 3046.1646728515625, - "top": 321.8039779663086 + "left": 2976.8598036984517, + "top": 94.1317307633906 }, "post_job_actions": { "TagDatasetActionstats": { @@ -2556,8 +2440,8 @@ } ], "position": { - "left": 3043.3521728515625, - "top": 497.5426254272461 + "left": 2978.758659528405, + "top": 395.9246888647188 }, "post_job_actions": { "TagDatasetActionstats": { @@ -2610,7 +2494,7 @@ ], "position": { "left": 3373.210205078125, - "top": 0.0 + "top": 0 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -2729,9 +2613,9 @@ "when": null, "workflow_outputs": [ { - "label": null, + "label": "Assembly statistics", "output_name": "output", - "uuid": "28a5cbed-abe4-4c2d-98f5-2bd72ce90a0c" + "uuid": "a91ae955-004c-4326-b68a-83067a7524d7" } ] } @@ -2740,6 +2624,6 @@ "VGP", "Reviewed" ], - "uuid": "41efeec2-5b76-437e-a113-449139178af4", - "version": 0 + "uuid": "df411f12-521f-49a7-8c01-238304894a12", + "version": 7 } \ No newline at end of file From 3a2c5f18fa485d417501da3b28fa353dda2b4b6a Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 20 Sep 2023 17:10:01 +0200 Subject: [PATCH 03/13] Expose bloom filter integer parameter --- .../VGP-WF3-Assembly/Assembly-(WF3)-tests.yml | 1 + .../VGP-WF3-Assembly/Assembly-(WF3).ga | 458 ++++++++++-------- 2 files changed, 265 insertions(+), 194 deletions(-) diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml index 6c9cf1032..d06af0727 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml @@ -15,6 +15,7 @@ - class: File identifier: yeast_reads_sub1.fastq.gz location: https://www.dropbox.com/scl/fi/yqcm8bk4jws3iy4y9m24h/yeast_reads_sub1.fastq.gz?rlkey=p409i94qa24kbc93afcssffoi&dl=1 + Bits for Hifiasm bloom filter: 32 SAK input file (Optional): null Name of primary assembly: Primary Name of alternate assembly: Alternate diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga index 78dbb8189..7bd64382e 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga @@ -13,8 +13,9 @@ } ], "format-version": "0.1", + "release": "0.1", "license": "CC-BY-4.0", - "name": "Assembly (WF3) (imported from URL)", + "name": "Assembly (WF3)", "steps": { "0": { "annotation": "", @@ -98,11 +99,38 @@ "workflow_outputs": [] }, "3": { - "annotation": "", + "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.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, + "inputs": [ + { + "description": "Default 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.", + "name": "Bits for Hifiasm bloom filter" + } + ], + "label": "Bits for Hifiasm bloom filter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 86.29189931686403, + "top": 1132.56845624909 + }, + "tool_id": null, + "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_version": null, + "type": "parameter_input", + "uuid": "3ce6ecc2-3262-4695-b4ef-1a58f52a48bd", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, "inputs": [ { "description": "", @@ -124,11 +152,11 @@ "when": null, "workflow_outputs": [] }, - "4": { + "5": { "annotation": "", "content_id": null, "errors": null, - "id": 4, + "id": 5, "input_connections": {}, "inputs": [ { @@ -151,11 +179,11 @@ "when": null, "workflow_outputs": [] }, - "5": { + "6": { "annotation": "", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { @@ -178,11 +206,11 @@ "when": null, "workflow_outputs": [] }, - "6": { + "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", "errors": null, - "id": 6, + "id": 7, "input_connections": { "library|input_1": { "id": 0, @@ -229,11 +257,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1", "errors": null, - "id": 7, + "id": 8, "input_connections": { "infile": { "id": 2, @@ -274,14 +302,47 @@ "when": null, "workflow_outputs": [] }, - "8": { + "9": { + "annotation": "", + "content_id": "pick_value", + "errors": null, + "id": 9, + "input_connections": { + "style_cond|type_cond|pick_from_0|value": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 1226.1930634976964, + "top": 238.20563138810184 + }, + "post_job_actions": {}, + "tool_id": "pick_value", + "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"integer\", \"__current_case__\": 1, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"value\": \"37\"}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "ef31ebb9-5de0-4c65-a3c7-30624dbddc05", + "when": null, + "workflow_outputs": [] + }, + "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "errors": null, - 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"output_name": "integer_param" }, - "TagDatasetActioninteger_param": { - "action_arguments": { - "tags": "estimated_genome_size" - }, - "action_type": "TagDatasetAction", - "output_name": "integer_param" - } - }, - "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", - "type": "tool", - "uuid": "2915bf7f-75c0-49cc-8f6f-af13b4510f4e", - "when": null, - "workflow_outputs": [ { - "label": "Estimated Genome size", - "output_name": "integer_param", - "uuid": "28396392-6855-400b-a28c-6297d43b7e23" + "label": "Size Plot", + "output_name": "Size Plot", + "uuid": "e46888e6-9ae3-4310-9639-de1cdfff1871" } ] }, - "23": { + "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 23, + "id": 25, "input_connections": { "input_file": { - "id": 9, + "id": 12, "output_name": "primary_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -2415,18 +2485,18 @@ } ] }, - "24": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 24, + "id": 26, "input_connections": { "input_file": { - "id": 9, + "id": 12, "output_name": "alternate_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 22, + "id": 23, "output_name": "integer_param" } }, @@ -2472,14 +2542,14 @@ } ] }, - "25": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "errors": null, - "id": 25, + "id": 27, "input_connections": { "infile": { - "id": 23, + "id": 25, "output_name": "stats" } }, @@ -2517,14 +2587,14 @@ "when": null, "workflow_outputs": [] }, - "26": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "errors": null, - "id": 26, + "id": 28, "input_connections": { "infile": { - "id": 24, + "id": 26, "output_name": "stats" } }, @@ -2562,18 +2632,18 @@ "when": null, "workflow_outputs": [] }, - "27": { + "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "errors": null, - "id": 27, + "id": 29, "input_connections": { "infile1": { - "id": 25, + "id": 27, "output_name": "outfile" }, "infile2": { - "id": 26, + "id": 28, "output_name": "outfile" } }, @@ -2624,6 +2694,6 @@ "VGP", "Reviewed" ], - "uuid": "df411f12-521f-49a7-8c01-238304894a12", - "version": 7 -} \ No newline at end of file + "uuid": "5ad09956-e96d-4412-a6cf-8642efe63f1e", + "version": 3 +} From 1731c46404b5bf42cc1bb0bba4b9cf3dce3f2834 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 20 Sep 2023 18:54:07 +0200 Subject: [PATCH 04/13] Expression tool output is integer, i think? --- .../VGP-WF3-Assembly/Assembly-(WF3)-tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml index d06af0727..f1bec29f9 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml @@ -37,10 +37,10 @@ asserts: has_line: line: "# scaffolds 2" - Estimated Genome size: - asserts: - has_line: - line: "2288021" + # Estimated Genome size: + # asserts: + # has_line: + # line: "2288021" Assembly Stats on Primary assembly: asserts: has_line: From e3f8c16a5d15357b449e365ff5a2a1be5bac1ff8 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 20 Sep 2023 21:17:30 +0200 Subject: [PATCH 05/13] Drop multiqc html test, check if 'Estimated Genome size' works as int --- .../VGP-WF3-Assembly/Assembly-(WF3)-tests.yml | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml index f1bec29f9..f0867d2ee 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml +++ b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml @@ -20,11 +20,6 @@ Name of primary assembly: Primary Name of alternate assembly: Alternate outputs: - multiqc html report: - asserts: - has_size: - value : 345000000 - delta: 10000000 Hifiasm Primary assembly: asserts: has_n_lines: @@ -37,10 +32,7 @@ asserts: has_line: line: "# scaffolds 2" - # Estimated Genome size: - # asserts: - # has_line: - # line: "2288021" + Estimated Genome size: 2288021 Assembly Stats on Primary assembly: asserts: has_line: From 16dc5edfe2369464f35709e81af93c1cc0fd584c Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Fri, 22 Sep 2023 15:06:47 -0400 Subject: [PATCH 06/13] rename the workflow and remove unused test data --- .../.dockstore.yml | 0 .../Assembly-Hifi-only-VGP3-tests.yml} | 0 .../Assembly-Hifi-only-VGP3.ga} | 2 +- .../test-data/Estimated Genome size.expression.json | 1 - 4 files changed, 1 insertion(+), 2 deletions(-) rename workflows/VGP-assembly-v2/{VGP-WF3-Assembly => Assembly-Hifi-only-VGP3}/.dockstore.yml (100%) rename workflows/VGP-assembly-v2/{VGP-WF3-Assembly/Assembly-(WF3)-tests.yml => Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml} (100%) rename workflows/VGP-assembly-v2/{VGP-WF3-Assembly/Assembly-(WF3).ga => Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga} (99%) delete mode 100644 workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/.dockstore.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml similarity index 100% rename from workflows/VGP-assembly-v2/VGP-WF3-Assembly/.dockstore.yml rename to workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml similarity index 100% rename from workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3)-tests.yml rename to workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga similarity index 99% rename from workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga rename to workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 7bd64382e..1371ae621 100644 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/Assembly-(WF3).ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ "format-version": "0.1", "release": "0.1", "license": "CC-BY-4.0", - "name": "Assembly (WF3)", + "name": "Assembly-Hifi-only-VGP3", "steps": { "0": { "annotation": "", diff --git a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json b/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json deleted file mode 100644 index 3954aed74..000000000 --- a/workflows/VGP-assembly-v2/VGP-WF3-Assembly/test-data/Estimated Genome size.expression.json +++ /dev/null @@ -1 +0,0 @@ -2288021 \ No newline at end of file From 10133dc5d3e049011a57e83dae32faf4b436959f Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Fri, 22 Sep 2023 15:16:44 -0400 Subject: [PATCH 07/13] move test datasets from dropbox to zenodo --- .../Assembly-Hifi-only-VGP3-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index f0867d2ee..a9e87afb4 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -2,11 +2,11 @@ job: Meryl Database: class: File - location: https://www.dropbox.com/scl/fi/5jn73x616vmasf92dsxv0/Meryl-db.meryldb?rlkey=72vxi05ea3yqemxx2loupih70&dl=1 + location: https://zenodo.org/record/8371053/files/Meryl-db.meryldb?download=1 filetype: meryldb Genomescope Summary: class: File - location: https://www.dropbox.com/scl/fi/ysi3736m37ah34sw3k1ex/GenomeScope_Summary.txt?rlkey=2ks66rdhqcmpn4pdchziwyv0r&dl=1 + location: https://zenodo.org/record/8371053/files/GenomeScope_Summary.txt?download=1 filetype: txt Pacbio Reads Collection: class: Collection @@ -14,7 +14,7 @@ elements: - class: File identifier: yeast_reads_sub1.fastq.gz - location: https://www.dropbox.com/scl/fi/yqcm8bk4jws3iy4y9m24h/yeast_reads_sub1.fastq.gz?rlkey=p409i94qa24kbc93afcssffoi&dl=1 + location: https://zenodo.org/record/8371053/files/yeast_reads_sub1.fastq.gz?download=1 Bits for Hifiasm bloom filter: 32 SAK input file (Optional): null Name of primary assembly: Primary From 4e0a32421311f11c41cbf9b7075ee6c4a4dbe677 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Tue, 26 Sep 2023 12:21:15 -0400 Subject: [PATCH 08/13] addition of usable gfa files --- .../Assembly-Hifi-only-VGP3.ga | 319 +++++++++++++----- 1 file changed, 230 insertions(+), 89 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index 1371ae621..d17b47da1 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ "format-version": "0.1", "release": "0.1", "license": "CC-BY-4.0", - "name": "Assembly-Hifi-only-VGP3", + "name": "Assembly-Hifi-only-VGP3 (imported from uploaded file)", "steps": { "0": { "annotation": "", @@ -34,7 +34,7 @@ "outputs": [], "position": { "left": 0, - "top": 326.8891830444336 + "top": 684.5727767944336 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -61,7 +61,7 @@ "outputs": [], "position": { "left": 23.59375, - "top": 841.6476669311523 + "top": 1199.3312606811523 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -88,7 +88,7 @@ "outputs": [], "position": { "left": 13.59375, - "top": 986.3919906616211 + "top": 1344.075584411621 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -106,7 +106,7 @@ "input_connections": {}, "inputs": [ { - "description": "Default 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.", + "description": "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.", "name": "Bits for Hifiasm bloom filter" } ], @@ -115,7 +115,7 @@ "outputs": [], "position": { "left": 86.29189931686403, - "top": 1132.56845624909 + "top": 1490.25204999909 }, "tool_id": null, "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", @@ -141,8 +141,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 1959.3465576171875, - "top": 1142.784080505371 + "left": 1853.27734375, + "top": 982.8125 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -169,7 +169,7 @@ "outputs": [], "position": { "left": 3333.6646728515625, - "top": 788.2954330444336 + "top": 1145.9790267944336 }, "tool_id": null, "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}", @@ -196,7 +196,7 @@ "outputs": [], "position": { "left": 3371.6192626953125, - "top": 936.2357406616211 + "top": 1293.919334411621 }, "tool_id": null, "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}", @@ -232,7 +232,7 @@ ], "position": { "left": 304.3323974609375, - "top": 635.2130355834961 + "top": 992.8966293334961 }, "post_job_actions": { "TagDatasetActionout1": { @@ -250,7 +250,7 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": \" \", \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"35\", \"match_read_wildcards\": \" \", \"revcomp\": true}, \"filter_options\": {\"discard_trimmed\": true, \"discard_untrimmed\": false, \"minimum_length\": null, \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [{\"__index__\": 0, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT\"}, \"single_noindels\": false}, {\"__index__\": 1, \"anywhere_adapter_source\": {\"anywhere_adapter_source_list\": \"user\", \"__current_case__\": 0, \"anywhere_adapter_name\": \"\", \"anywhere_adapter\": \"ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT\"}, \"single_noindels\": false}], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.0+galaxy1", "type": "tool", "uuid": "f679b5eb-cc26-4005-9499-3ad2eb4698d4", @@ -279,7 +279,7 @@ ], "position": { "left": 1007.3011474609375, - "top": 1171.221580505371 + "top": 1528.905174255371 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -324,7 +324,7 @@ ], "position": { "left": 1226.1930634976964, - "top": 238.20563138810184 + "top": 595.8892251381019 }, "post_job_actions": {}, "tool_id": "pick_value", @@ -361,7 +361,7 @@ ], "position": { "left": 749.6564364957525, - "top": 692.448333004384 + "top": 1050.131926754384 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", @@ -411,7 +411,7 @@ ], "position": { "left": 1150.2698974609375, - "top": 1005.8806381225586 + "top": 1363.5642318725586 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -449,12 +449,7 @@ "output_name": "out1" } }, - "inputs": [ - { - "description": "runtime parameter for tool Hifiasm", - "name": "mode" - } - ], + "inputs": [], "label": null, "name": "Hifiasm", "outputs": [ @@ -485,7 +480,7 @@ ], "position": { "left": 1673.8636169433594, - "top": 158.73578643798828 + "top": 516.4193801879883 }, "post_job_actions": { "TagDatasetActionalternate_contig_graph": { @@ -531,7 +526,7 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"blank\", \"__current_case__\": 0}, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"RuntimeValue\"}}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"advanced_selector\": \"blank\", \"__current_case__\": 0}, \"assembly_options\": {\"assembly_selector\": \"blank\", \"__current_case__\": 0}, \"filter_bits\": {\"__class__\": \"ConnectedValue\"}, \"hic_partition\": {\"hic_partition_selector\": \"blank\", \"__current_case__\": 0}, \"log_out\": true, \"mode\": {\"mode_selector\": \"standard\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}}, \"purge_options\": {\"purge_selector\": \"set\", \"__current_case__\": 1, \"purge_level\": \"0\", \"similarity_threshold\": \"0.75\", \"minimum_overlap\": \"1\", \"purge_max\": null, \"n_hap\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.16.1+galaxy4", "type": "tool", "uuid": "cecbcd76-97f0-4e7a-9c90-061d3e5be432", @@ -571,7 +566,7 @@ ], "position": { "left": 1303.2670459747314, - 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"id": 18, + "id": 20, "output_name": "out_file1" } }, @@ -1849,7 +1990,7 @@ ], "position": { "left": 1742.6988525390625, - "top": 791.9460067749023 + "top": 1149.6296005249023 }, "post_job_actions": { "RenameDatasetActioninteger_param": { @@ -1881,12 +2022,12 @@ } ] }, - "24": { + "26": { "annotation": "", - "id": 24, + "id": 26, "input_connections": { "Alternate data": { - "id": 22, + "id": 24, "input_subworkflow_step_id": 1, "output_name": "gfastats data for plotting" }, @@ -1901,7 +2042,7 @@ "output_name": "output" }, "Primary data": { - "id": 21, + "id": 23, "input_subworkflow_step_id": 0, "output_name": "gfastats data for plotting" } @@ -1912,7 +2053,7 @@ "outputs": [], "position": { "left": 4197.244140625, - "top": 559.7442855834961 + "top": 917.4278793334961 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2428,18 +2569,18 @@ } ] }, - "25": { + "27": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 25, + "id": 27, "input_connections": { "input_file": { "id": 12, "output_name": "primary_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 23, + "id": 25, "output_name": "integer_param" } }, @@ -2454,7 +2595,7 @@ ], "position": { "left": 2976.8598036984517, - "top": 94.1317307633906 + "top": 451.8153245133906 }, "post_job_actions": { "TagDatasetActionstats": { @@ -2485,18 +2626,18 @@ } ] }, - "26": { + "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, - "id": 26, + "id": 28, "input_connections": { "input_file": { "id": 12, "output_name": "alternate_contig_graph" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 23, + "id": 25, "output_name": "integer_param" } }, @@ -2511,7 +2652,7 @@ ], "position": { "left": 2978.758659528405, - "top": 395.9246888647188 + "top": 753.6082826147187 }, "post_job_actions": { "TagDatasetActionstats": { @@ -2542,14 +2683,14 @@ } ] }, - 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"id": 29, + "id": 31, "input_connections": { "infile1": { - "id": 27, + "id": 29, "output_name": "outfile" }, "infile2": { - "id": 28, + "id": 30, "output_name": "outfile" } }, @@ -2658,7 +2799,7 @@ ], "position": { "left": 3697.38623046875, - "top": 203.26703643798828 + "top": 560.9506301879883 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -2694,6 +2835,6 @@ "VGP", "Reviewed" ], - "uuid": "5ad09956-e96d-4412-a6cf-8642efe63f1e", + "uuid": "166e7ec4-d3f1-4e18-b81b-2559e7fb2e76", "version": 3 -} +} \ No newline at end of file From e144e23d7a6937d4ff44ca8e697e20f82499f2ae Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Tue, 26 Sep 2023 12:22:31 -0400 Subject: [PATCH 09/13] removing 'imported from file' from the title --- .../Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index d17b47da1..e9e36874a 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -15,7 +15,7 @@ "format-version": "0.1", "release": "0.1", "license": "CC-BY-4.0", - "name": "Assembly-Hifi-only-VGP3 (imported from uploaded file)", + "name": "Assembly-Hifi-only-VGP3", "steps": { "0": { "annotation": "", From b4a2c2e35edef81ed0358fe68e4a6397e21da578 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Tue, 26 Sep 2023 13:42:47 -0400 Subject: [PATCH 10/13] changed a test that was failing the linting --- .../Assembly-Hifi-only-VGP3-tests.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index a9e87afb4..d9ce66700 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -32,7 +32,10 @@ asserts: has_line: line: "# scaffolds 2" - Estimated Genome size: 2288021 + Estimated Genome size: + asserts: + has_line: + line: "2288021" Assembly Stats on Primary assembly: asserts: has_line: From 5945010181d005e7f72c4aff8cba5cc19a9f9593 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Tue, 26 Sep 2023 13:48:40 -0400 Subject: [PATCH 11/13] Addition of the README and the CHANGELOG --- .../Assembly-Hifi-only-VGP3/CHANGELOG.md | 12 ++++++++ .../Assembly-Hifi-only-VGP3/README.md | 29 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md create mode 100644 workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md new file mode 100644 index 000000000..8da723196 --- /dev/null +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md @@ -0,0 +1,12 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +## [0.1] - 2023-09-26 + +Addition of the workflow to the iwc repository. diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md new file mode 100644 index 000000000..d6e3cb90f --- /dev/null +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md @@ -0,0 +1,29 @@ +## Contiging Solo w/HiC: + +Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing. + + +### Inputs + + +1. Hifi long reads [fastq] +2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq] +3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq] +4. K-mer database [meryldb] +5. Genome profile summary generated by Genomescope [txt] +6. Name of first assembly +7. Name of second assembly + + +### Outputs + +1. Haplotype 1 assembly +2. Haplotype 2 assembly +3. QC: BUSCO report for both assemblies +4. QC: Merqury report for both assemblies +5. QC: Assembly statistics for both assemblies +6. QC: Nx plot for both assemblies +7. QC: Size plot for both assemblie + + + From f76b0bbb067e66b23d86de6086ec13daf8b19f96 Mon Sep 17 00:00:00 2001 From: Delphine-L Date: Wed, 27 Sep 2023 11:33:56 -0400 Subject: [PATCH 12/13] correcting the test for genome size --- .../Assembly-Hifi-only-VGP3-tests.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index d9ce66700..a9e87afb4 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -32,10 +32,7 @@ asserts: has_line: line: "# scaffolds 2" - Estimated Genome size: - asserts: - has_line: - line: "2288021" + Estimated Genome size: 2288021 Assembly Stats on Primary assembly: asserts: has_line: From ad6dd49b6000ab5eb9288e3723eaeb33f61342d8 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 6 Oct 2023 12:19:41 -0400 Subject: [PATCH 13/13] Fix .dockstore.yml and other minor things --- .../VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml | 4 ++-- .../Assembly-Hifi-only-VGP3-tests.yml | 4 ++-- .../Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga | 6 +++--- workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md | 3 --- 4 files changed, 7 insertions(+), 10 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml index 6f7bce702..5afda4dc5 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/.dockstore.yml @@ -1,7 +1,7 @@ version: 1.2 workflows: - name: main - primaryDescriptorPath: /Assembly-(WF3).ga + primaryDescriptorPath: /Assembly-Hifi-only-VGP3.ga subclass: Galaxy testParameterFiles: - - /Assembly-(WF3)-tests.yml + - /Assembly-Hifi-only-VGP3-tests.yml diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml index a9e87afb4..6e86e5aa1 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3-tests.yml @@ -1,4 +1,4 @@ -- doc: Test outline for Assembly-(WF3) +- doc: Test for Assembly-Hifi-only-VGP3 job: Meryl Database: class: File @@ -24,7 +24,7 @@ asserts: has_n_lines: n: 174 - HIfiasm Alternate assembly: + Hifiasm Alternate assembly: asserts: has_n_lines: n: 4 diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga index e9e36874a..1ab20a42b 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga @@ -831,7 +831,7 @@ "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { - "newname": "HIfiasm Alternate assembly" + "newname": "Hifiasm Alternate assembly" }, "action_type": "RenameDatasetAction", "output_name": "output" @@ -865,7 +865,7 @@ "when": null, "workflow_outputs": [ { - "label": "HIfiasm Alternate assembly", + "label": "Hifiasm Alternate assembly", "output_name": "output", "uuid": "76bc77a2-fd89-494d-a646-091560aeb1a1" } @@ -2837,4 +2837,4 @@ ], "uuid": "166e7ec4-d3f1-4e18-b81b-2559e7fb2e76", "version": 3 -} \ No newline at end of file +} diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md index d6e3cb90f..47180d7c5 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/README.md @@ -24,6 +24,3 @@ Generate phased assembly based on PacBio Hifi Reads using HiC data from the same 5. QC: Assembly statistics for both assemblies 6. QC: Nx plot for both assemblies 7. QC: Size plot for both assemblie - - -