From 7cd6935f478fd5a2969b4a873f741a969042a40d Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 25 Oct 2024 11:00:05 +0200 Subject: [PATCH 1/5] first release of RNAseq DE analysis, filtering and plotting workflow --- .../transcriptomics/rnaseq-de/.dockstore.yml | 11 + .../transcriptomics/rnaseq-de/CHANGELOG.md | 3 + workflows/transcriptomics/rnaseq-de/README.md | 20 + .../rnaseq-de-filtering-plotting-tests.yml | 53 + .../rnaseq-de/rnaseq-de-filtering-plotting.ga | 953 +++ .../rnaseq-de/test-data/SRR5085167.tabular | 7128 +++++++++++++++++ .../rnaseq-de/test-data/SRR5085168.tabular | 7128 +++++++++++++++++ .../rnaseq-de/test-data/SRR5085169.tabular | 7128 +++++++++++++++++ .../rnaseq-de/test-data/SRR5085170.tabular | 7128 +++++++++++++++++ 9 files changed, 29552 insertions(+) create mode 100644 workflows/transcriptomics/rnaseq-de/.dockstore.yml create mode 100644 workflows/transcriptomics/rnaseq-de/CHANGELOG.md create mode 100644 workflows/transcriptomics/rnaseq-de/README.md create mode 100644 workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml create mode 100644 workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga create mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085167.tabular create mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085168.tabular create mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085169.tabular create mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular diff --git a/workflows/transcriptomics/rnaseq-de/.dockstore.yml b/workflows/transcriptomics/rnaseq-de/.dockstore.yml new file mode 100644 index 000000000..2da18cb69 --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/.dockstore.yml @@ -0,0 +1,11 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /rnaseq-de-filtering-plotting.ga + testParameterFiles: + - /rnaseq-de-filtering-plotting-tests.yml + authors: + - name: Pavankumar Videm + orcid: 0000-0002-5192-126X diff --git a/workflows/transcriptomics/rnaseq-de/CHANGELOG.md b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md new file mode 100644 index 000000000..4ff503093 --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md @@ -0,0 +1,3 @@ +## [0.1] 2024-10-25 + +First release. diff --git a/workflows/transcriptomics/rnaseq-de/README.md b/workflows/transcriptomics/rnaseq-de/README.md new file mode 100644 index 000000000..f9c32442a --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/README.md @@ -0,0 +1,20 @@ +# RNA-seq Differential expression and filtering workflow + +## Inputs dataset + +- The workflow takes two collections of count files, each correcsponds to an experimental condition +- Gene Annotaton: The same GTF file used for mapping and quantification. It is used to annotate the DESeq2 results table. Ideally, the GTF file should contain `gene_id`, `gene_biotype` and `gene_name` attributes. + +## Inputs values + +- Adjusted p-value threshold: All the genes with an adjusted p-value less than this value are considered as differentially expressed. With a value of 0.05, expect 5% of false positives in the differentially expressed genes list. +- log2 fold change threshold: All the genes with an absolute fold cahnge (regarless of up or down regulation) more than this value are selected. + + +## Processing + +- The workflow uses DESeq2 for performing differential expression analysis. In addition to the results table, it also produces normalized counts table. +- The results table is annotated with gene positions, biotypes, gene symbols. +- The annotated results table is further filtered with the input adjusted p-value and log2 fold cahnge thresholds. +- A valcano plot is generated with top 10 significantly differentially expressed genes. +- A heatmap of log trasformed normalized counts and another heatmap of Z-scores is generated. diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml new file mode 100644 index 000000000..be4303b20 --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml @@ -0,0 +1,53 @@ +- doc: Test outline for rnaseq-de-filtering-plotting + job: + Gene Annotaton: + class: File + location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf + filetype: gtf + Main factor counts: + class: Collection + collection_type: list + elements: + - class: File + identifier: SRR5085169 Counts Table + path: test-data/SRR5085169.tabular + - class: File + identifier: SRR5085170 Counts Table + path: test-data/SRR5085170.tabular + Base factor counts: + class: Collection + collection_type: list + elements: + - class: File + identifier: SRR5085167 Counts Table + path: test-data/SRR5085167.tabular + - class: File + identifier: SRR5085168 Counts Table + path: test-data/SRR5085168.tabular + Adjusted p-value threshold: '0.1' + log2 fold change threshold: '0.5' + outputs: + Annotated DESeq2 results table: + has_text_matching: + expression: "YML123C\t122.984408142053\t-1.67[0-9]*\t0.21[0-9]*\t-7.66[0-9]*\t1.81[0-9]*e-14\t5.04[0-9]*e-[0-9]*\tchrXIII\t24036\t25800\t-\tprotein_coding\tPHO84" + expression: "YKL081W\t264.71[0-9]*\t-0.54[0-9]*\t0.15[0-9]*\t-3.46[0-9]*\t0.00[0-9]*\t0.09[0-9]*\tchrXI\t282890\t284455\t+\tprotein_coding\tTEF4" + Heatmap of Z-scores: + has_size: + value: 19510 + delta: 1000 + DESeq2 Normalized Counts: + has_text_matching: + expression: "YML123C\t210.50[0-9]*\t180.36[0-9]*\t48.64[0-9]*\t52.43[0-9]*" + expression: "YKL081W\t313.76[0-9]*\t322.37[0-9]*\t223.48[0-9]*\t199.24[0-9]*" + DESeq2 Plots: + has_size: + value: 1193021 + delta: 60000 + Volcano Plot: + has_size: + value: 301346 + delta: 15000 + Heatmap of log transformed normalized counts: + has_size: + value: 19501 + delta: 1000 diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga new file mode 100644 index 000000000..712f94c40 --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -0,0 +1,953 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "This workflow takes two collections of count tables as input and performs differential expression analysis.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" + } + ], + "format-version": "0.1", + "license": "MIT", + "release": "0.1", + "name": "rnaseq-de-filtering-plotting", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "Adjusted p-value threshold to call genes as differentially expressed", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "Adjusted p-value threshold to call genes as differentially expressed", + "name": "Adjusted p-value threshold" + } + ], + "label": "Adjusted p-value threshold", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0, + "top": 334.9853794406297 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"float\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "43754055-ab65-475e-ae75-b84be92f9a06", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c9379396-b89c-4376-9805-bd148f2d6522" + } + ] + }, + "1": { + "annotation": "The same annotation GTF used for mapping and counting", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "The same annotation GTF used for mapping and counting", + "name": "Gene Annotaton" + } + ], + "label": "Gene Annotaton", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 280.0001152778115, + "top": 396.9853794406297 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "4f6df6ae-39ac-4a5e-98df-a0cb082a44fe", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "Counts from your main factor of interest. 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0 +tS(UGA)Q2 0 +Q0110 0 +Q0120 0 +tH(GUG)Q 0 +Q0050 0 +tA(UGC)Q 0 +Q0085 0 +Q0182 0 +tM(CAU)Q1 0 +tS(GCU)Q1 0 +tV(UAC)Q 0 +tQ(UUG)Q 0 +tR(UCU)Q1 0 +Q0060 0 +Q0045 0 +tP(UGG)Q 0 +tI(GAU)Q 0 +Q0158 0 diff --git a/workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular b/workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular new file mode 100644 index 000000000..dd03db31e --- /dev/null +++ b/workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular @@ -0,0 +1,7128 @@ +Geneid SRR5085170 +YDL246C 0 +YDL243C 0 +YDR387C 6 +YDL094C 0 +YDR438W 0 +YDR523C 1 +YDR542W 0 +YDR492W 9 +YDR018C 0 +YDL189W 5 +YDR508C 47 +YDR462W 1 +YDR175C 5 +YDR186C 7 +YDR150W 35 +YDR243C 8 +YDL182W 36 +YDR362C 9 +YDR232W 22 +YDR158W 102 +YDR439W 3 +YDL206W 7 +YDR125C 0 +YDR338C 7 +YDR526C 0 +YDR533C 10 +YDR272W 13 +YDR197W 4 +YDR512C 3 +YDR489W 4 +YDR299W 27 +YDL015C 26 +YDR304C 40 +YDR271C 0 +YDL181W 2 +YDR367W 21 +YDR085C 4 +YDL097C 49 +YDL139C 0 +YDR200C 7 +YDR191W 4 +YDR451C 6 +YDR469W 3 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+tI(GAU)Q 0 +Q0158 0 From ad0df1e0d00e9682b4503bdbe180acf724e624e3 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Sat, 26 Oct 2024 13:21:26 +0200 Subject: [PATCH 2/5] Make thresholds optional, header param, better descriptions --- workflows/transcriptomics/rnaseq-de/README.md | 13 +- .../rnaseq-de-filtering-plotting-tests.yml | 9 +- .../rnaseq-de/rnaseq-de-filtering-plotting.ga | 609 ++++++++++-------- 3 files changed, 367 insertions(+), 264 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-de/README.md b/workflows/transcriptomics/rnaseq-de/README.md index f9c32442a..1ead394fc 100644 --- a/workflows/transcriptomics/rnaseq-de/README.md +++ b/workflows/transcriptomics/rnaseq-de/README.md @@ -1,20 +1,23 @@ # RNA-seq Differential expression and filtering workflow +This workflow works only with an experimental setup containing exactly 2 conditions with at least 2 replicates per condition. + ## Inputs dataset -- The workflow takes two collections of count files, each correcsponds to an experimental condition +- Counts from changed condition: Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples. +- Counts from reference condition: Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples. - Gene Annotaton: The same GTF file used for mapping and quantification. It is used to annotate the DESeq2 results table. Ideally, the GTF file should contain `gene_id`, `gene_biotype` and `gene_name` attributes. ## Inputs values -- Adjusted p-value threshold: All the genes with an adjusted p-value less than this value are considered as differentially expressed. With a value of 0.05, expect 5% of false positives in the differentially expressed genes list. -- log2 fold change threshold: All the genes with an absolute fold cahnge (regarless of up or down regulation) more than this value are selected. - +- Count files have header: Indicate whether your input count files have a header line. Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have. +- Adjusted p-value threshold: All the genes with an adjusted p-value less than this value are considered as differentially expressed. With a value of 0.05, expect 5% of false positives in the differentially expressed genes list. If empty, a default value of 0.05 is used. +- log2 fold change threshold: All the genes with an absolute fold change (regarless of up or down regulation) more than this value are selected. A log2 FC of 3 equals to an absolute fold change of 8 (2³). If empty, a default value of 1.0 is used. ## Processing - The workflow uses DESeq2 for performing differential expression analysis. In addition to the results table, it also produces normalized counts table. - The results table is annotated with gene positions, biotypes, gene symbols. -- The annotated results table is further filtered with the input adjusted p-value and log2 fold cahnge thresholds. +- The annotated results table is further filtered with the input adjusted p-value and log2 fold change thresholds. - A valcano plot is generated with top 10 significantly differentially expressed genes. - A heatmap of log trasformed normalized counts and another heatmap of Z-scores is generated. diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml index be4303b20..bffcb4356 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml @@ -1,10 +1,10 @@ -- doc: Test outline for rnaseq-de-filtering-plotting +- doc: Test outline for RNAseq_DE_filtering_plotting job: Gene Annotaton: class: File location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf - Main factor counts: + Counts from changed condition: class: Collection collection_type: list elements: @@ -14,7 +14,7 @@ - class: File identifier: SRR5085170 Counts Table path: test-data/SRR5085170.tabular - Base factor counts: + Counts from reference condition: class: Collection collection_type: list elements: @@ -24,6 +24,7 @@ - class: File identifier: SRR5085168 Counts Table path: test-data/SRR5085168.tabular + Count files have header: true Adjusted p-value threshold: '0.1' log2 fold change threshold: '0.5' outputs: @@ -43,7 +44,7 @@ has_size: value: 1193021 delta: 60000 - Volcano Plot: + Volcano Plot of DE genes: has_size: value: 301346 delta: 15000 diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga index 712f94c40..74bfad29c 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes two collections of count tables as input and performs differential expression analysis.", + "annotation": "This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.\n", "comments": [], "creator": [ { @@ -12,155 +12,143 @@ "format-version": "0.1", "license": "MIT", "release": "0.1", - "name": "rnaseq-de-filtering-plotting", + "name": "RNAseq_DE_filtering_plotting", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, "steps": { "0": { - "annotation": "Adjusted p-value threshold to call genes as differentially expressed", + "annotation": "Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples.", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Adjusted p-value threshold to call genes as differentially expressed", - "name": "Adjusted p-value threshold" + "description": "Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples.", + "name": "Counts from changed condition" } ], - "label": "Adjusted p-value threshold", - "name": "Input parameter", + "label": "Counts from changed condition", + "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 334.9853794406297 + "top": 231.6810606846659 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"float\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "43754055-ab65-475e-ae75-b84be92f9a06", + "type": "data_collection_input", + "uuid": "7e7436a6-e408-4941-81c2-7a86c0c9235a", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c9379396-b89c-4376-9805-bd148f2d6522" - } - ] + "workflow_outputs": [] }, "1": { - "annotation": "The same annotation GTF used for mapping and counting", + "annotation": "Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples.", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "The same annotation GTF used for mapping and counting", - "name": "Gene Annotaton" + "description": "Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples.", + "name": "Counts from reference condition" } ], - "label": "Gene Annotaton", - "name": "Input dataset", + "label": "Counts from reference condition", + "name": "Input dataset collection", "outputs": [], "position": { - "left": 280.0001152778115, - "top": 396.9853794406297 + "left": 47.54331804667683, + "top": 344.2691910956221 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, - "type": "data_input", - "uuid": "4f6df6ae-39ac-4a5e-98df-a0cb082a44fe", + "type": "data_collection_input", + "uuid": "2f811a41-c4af-4661-b17b-76ee244f3b27", "when": null, "workflow_outputs": [] }, "2": { - "annotation": "Counts from your main factor of interest. For eg. counts from treatment or knockdown samples.", + "annotation": "Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have.", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Counts from your main factor of interest. For eg. counts from treatment or knockdown samples.", - "name": "Main factor counts" + "description": "Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have.", + "name": "Count files have header" } ], - "label": "Main factor counts", - "name": "Input dataset collection", + "label": "Count files have header", + "name": "Input parameter", "outputs": [], "position": { - "left": 0, - "top": 559.9853794406297 + "left": 110.4753923836675, + "top": 456.18541400369907 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, - "type": "data_collection_input", - "uuid": "7e7436a6-e408-4941-81c2-7a86c0c9235a", + "type": "parameter_input", + "uuid": "7eeb1fbf-cacd-4395-a22f-cceaeab27079", "when": null, "workflow_outputs": [] }, "3": { - "annotation": "Adjusted p-value threshold to call genes as differentially expressed", + "annotation": "The same annotation GTF used for mapping and counting", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Adjusted p-value threshold to call genes as differentially expressed", - "name": "log2 fold change threshold" + "description": "The same annotation GTF used for mapping and counting", + "name": "Gene Annotaton" } ], - "label": "log2 fold change threshold", - "name": "Input parameter", + "label": "Gene Annotaton", + "name": "Input dataset", "outputs": [], "position": { - "left": 560.0000842814684, - "top": 272.9853794406297 + "left": 153.82812224613164, + "top": 585.5486767979796 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"float\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, - "type": "parameter_input", - "uuid": "bb8bb582-3f12-4dfd-b973-2e24bf6aea07", + "type": "data_input", + "uuid": "4f6df6ae-39ac-4a5e-98df-a0cb082a44fe", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2af4c81d-65c3-40d7-91d4-05550fe09541" - } - ] + "workflow_outputs": [] }, "4": { - "annotation": "Counts from the base factor of interest. For eg. counts from untreated or wildtype samples.", + "annotation": "Adjusted p-value threshold to call genes as differentially expressed. If not set, default 0.05 is used.", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "Counts from the base factor of interest. For eg. counts from untreated or wildtype samples.", - "name": "Base factor counts" + "description": "Adjusted p-value threshold to call genes as differentially expressed. 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\"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"6\", \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.6", + "type": "tool", + "uuid": "cb314a3d-0b05-4d45-a961-591d59b3852b", + "when": null, + "workflow_outputs": [ + { + "label": "Volcano Plot of DE genes", + "output_name": "plot", + "uuid": "9c1cd777-caa5-4477-8a24-9708480bd693" + } + ] + }, + "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 16, + "id": 19, "input_connections": { "components_1|param_type|component_value": { - "id": 14, + "id": 16, "output_name": "text_param" } }, @@ -693,8 +785,8 @@ } ], "position": { - "left": 1623.0703058756483, - "top": 875.9741497462079 + "left": 2144.7794821932416, + "top": 725.294415795629 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", @@ -711,23 +803,23 @@ "when": null, "workflow_outputs": [] }, - "17": { + "20": { "annotation": "", "content_id": "Filter1", "errors": null, - "id": 17, + "id": 20, "input_connections": { "cond": { - "id": 7, + "id": 12, "output_name": "out1" }, "input": { - "id": 15, + "id": 17, "output_name": "out_file1" } }, "inputs": [], - "label": null, + "label": "Filter with log2 FC threshold", "name": "Filter", "outputs": [ { @@ -736,13 +828,13 @@ } ], "position": { - "left": 1440.023974769488, - "top": 151.77137869452596 + "left": 1910.07823962931, + "top": 474.9743920452724 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { - "newname": "Genes with significant adj p-value & abs(log2(FC)) > 1" + "newname": "Genes filtered with adj p-value and log2(FC) thresholds" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" @@ -754,20 +846,26 @@ "type": "tool", "uuid": "1f787252-7a94-43b6-bb66-9624923ed05c", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "Significantly differentially expressed genes", + "output_name": "out_file1", + "uuid": "ca9ba83d-00e7-4778-a670-9a5605606cfc" + } + ] }, - "18": { + "21": { "annotation": "", "content_id": "join1", "errors": null, - "id": 18, + "id": 21, "input_connections": { "input1": { - "id": 8, + "id": 10, "output_name": "counts_out" }, "input2": { - "id": 17, + "id": 20, "output_name": "out_file1" } }, @@ -781,8 +879,8 @@ } ], "position": { - "left": 1690.000350360508, - "top": 696.9853794406297 + "left": 2271.404780182028, + "top": 406.30668475687355 }, "post_job_actions": {}, "tool_id": "join1", @@ -793,18 +891,18 @@ "when": null, "workflow_outputs": [] }, - "19": { + "22": { "annotation": "", "content_id": "Cut1", "errors": null, - "id": 19, + "id": 22, "input_connections": { "columnList": { - "id": 16, + "id": 19, "output_name": "out1" }, "input": { - "id": 18, + "id": 21, "output_name": "out_file1" } }, @@ -818,8 +916,8 @@ } ], "position": { - "left": 1970.000416880268, - "top": 721.9853794406297 + "left": 2560.320455929024, + "top": 649.1552708097212 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -838,19 +936,19 @@ "when": null, "workflow_outputs": [] }, - "20": { + "23": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0", "errors": null, - "id": 20, + "id": 23, "input_connections": { "input1": { - "id": 19, + "id": 22, "output_name": "out_file1" } }, "inputs": [], - "label": null, + "label": "Generate Heatmap of counts", "name": "heatmap2", "outputs": [ { @@ -859,8 +957,8 @@ } ], "position": { - "left": 2250.000483400028, - "top": 699.9853794406297 + "left": 2874.905386062883, + "top": 454.7381454908998 }, "post_job_actions": { "RenameDatasetActionoutput1": { @@ -891,19 +989,19 @@ } ] }, - "21": { + "24": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0", "errors": null, - "id": 21, + "id": 24, "input_connections": { "input1": { - "id": 19, + "id": 22, "output_name": "out_file1" } }, "inputs": [], - "label": null, + "label": "Generate Heatmap of Z-scores", "name": "heatmap2", "outputs": [ { @@ -912,8 +1010,8 @@ } ], "position": { - "left": 2250.000483400028, - "top": 955.9853794406297 + "left": 2899.706231952903, + "top": 852.4572467969889 }, "post_job_actions": { "RenameDatasetActionoutput1": { @@ -946,8 +1044,9 @@ } }, "tags": [ - "transcriptomics" + "transcriptomics", + "RNAseq" ], - "uuid": "dcf545b8-ed1b-483f-8dd1-80d46b180cf6", - "version": 7 + "uuid": "5238edf7-3eee-491f-9e91-d43a0bdc4533", + "version": 14 } \ No newline at end of file From 6844577f18a1c78fc310876d9a10d727d72b7e6b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 8 Nov 2024 14:46:04 +0100 Subject: [PATCH 3/5] hide unnecessary outputs and move count files to Zenodo --- .../rnaseq-de-filtering-plotting-tests.yml | 14 +-- .../rnaseq-de/rnaseq-de-filtering-plotting.ga | 115 +++++++++++++++--- 2 files changed, 105 insertions(+), 24 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml index bffcb4356..f7cae70a6 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting-tests.yml @@ -2,7 +2,7 @@ job: Gene Annotaton: class: File - location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf + location: https://zenodo.org/records/14056162/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf Counts from changed condition: class: Collection @@ -10,23 +10,23 @@ elements: - class: File identifier: SRR5085169 Counts Table - path: test-data/SRR5085169.tabular + location: https://zenodo.org/records/14056162/files/SRR5085169.tabular - class: File identifier: SRR5085170 Counts Table - path: test-data/SRR5085170.tabular + location: https://zenodo.org/records/14056162/files/SRR5085170.tabular Counts from reference condition: class: Collection collection_type: list elements: - class: File identifier: SRR5085167 Counts Table - path: test-data/SRR5085167.tabular + location: https://zenodo.org/records/14056162/files/SRR5085167.tabular - class: File identifier: SRR5085168 Counts Table - path: test-data/SRR5085168.tabular + location: https://zenodo.org/records/14056162/files/SRR5085168.tabular Count files have header: true - Adjusted p-value threshold: '0.1' - log2 fold change threshold: '0.5' + Adjusted p-value threshold: 0.1 + log2 fold change threshold: 0.5 outputs: Annotated DESeq2 results table: has_text_matching: diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga index 74bfad29c..5dee8302b 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -11,7 +11,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", "name": "RNAseq_DE_filtering_plotting", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -171,7 +170,13 @@ "left": 812.5163140349712, "top": 0 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { "changeset_revision": "86755160afbf", @@ -237,7 +242,13 @@ "left": 450.98839299501634, "top": 659.5669461166157 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionfloat_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "float_param" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "tool_shed_repository": { "changeset_revision": "b19e21af9c52", @@ -276,7 +287,13 @@ "left": 1065.0285936858018, "top": 27.545761768432413 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "tool_shed_repository": { "changeset_revision": "86755160afbf", @@ -315,7 +332,13 @@ "left": 497.8587064818947, "top": 824.4797977763942 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionfloat_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "float_param" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "tool_shed_repository": { "changeset_revision": "b19e21af9c52", @@ -383,7 +406,13 @@ "left": 741.3738148942634, "top": 199.67185694924424 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActiondeseq_out": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "deseq_out" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "tool_shed_repository": { "changeset_revision": "8fe98f7094de", @@ -433,7 +462,13 @@ "left": 1030.3831032381008, "top": 646.2395043126207 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "tool_shed_repository": { "changeset_revision": "e188c9826e0f", @@ -472,7 +507,13 @@ "left": 1037.5832128440811, "top": 834.4804304279605 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "tool_shed_repository": { "changeset_revision": "e188c9826e0f", @@ -515,7 +556,13 @@ "left": 1053.2118356859382, "top": 253.53181990473982 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutput": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0", "tool_shed_repository": { "changeset_revision": "e98d4ab5b5bc", @@ -554,7 +601,13 @@ "left": 1444.0049932961922, "top": 643.7692280168025 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { "changeset_revision": "86755160afbf", @@ -654,10 +707,16 @@ } ], "position": { - "left": 1795.1067951362936, - "top": 744.8872464237379 + "left": 1795.8106940526452, + "top": 744.1580154160025 + }, + "post_job_actions": { + "HideDatasetActiontext_param": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "text_param" + } }, - "post_job_actions": {}, "tool_id": "param_value_from_file", "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"text\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", @@ -695,6 +754,11 @@ "top": 371.3592826475832 }, "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Genes filtered with adj p-value threshold" @@ -788,7 +852,13 @@ "left": 2144.7794821932416, "top": 725.294415795629 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionout1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out1" + } + }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "tool_shed_repository": { "changeset_revision": "e188c9826e0f", @@ -882,7 +952,13 @@ "left": 2271.404780182028, "top": 406.30668475687355 }, - "post_job_actions": {}, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, "tool_id": "join1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/dm6.len\", \"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.1.3", @@ -920,6 +996,11 @@ "top": 649.1552708097212 }, "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + }, "RenameDatasetActionout_file1": { "action_arguments": { "newname": "Normalized counts for the most differentially expressed genes" @@ -1047,6 +1128,6 @@ "transcriptomics", "RNAseq" ], - "uuid": "5238edf7-3eee-491f-9e91-d43a0bdc4533", - "version": 14 + "uuid": "15d188a7-b028-4cf7-bb5d-13858e1f6e78", + "version": 15 } \ No newline at end of file From e37a207e45ac66a77ee5b1bc4c350ec4d7855cb6 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 8 Nov 2024 14:47:06 +0100 Subject: [PATCH 4/5] add release --- .../transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga index 5dee8302b..96c426aab 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -11,6 +11,7 @@ ], "format-version": "0.1", "license": "MIT", + "release": "0.1", "name": "RNAseq_DE_filtering_plotting", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" From 0c49c70c876585bff1648ca5b5f7e125ed614ba9 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 8 Nov 2024 14:50:26 +0100 Subject: [PATCH 5/5] remove test data --- .../rnaseq-de/test-data/SRR5085167.tabular | 7128 ----------------- .../rnaseq-de/test-data/SRR5085168.tabular | 7128 ----------------- .../rnaseq-de/test-data/SRR5085169.tabular | 7128 ----------------- .../rnaseq-de/test-data/SRR5085170.tabular | 7128 ----------------- 4 files changed, 28512 deletions(-) delete mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085167.tabular delete mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085168.tabular delete mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085169.tabular delete mode 100644 workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular diff --git a/workflows/transcriptomics/rnaseq-de/test-data/SRR5085167.tabular b/workflows/transcriptomics/rnaseq-de/test-data/SRR5085167.tabular deleted file mode 100644 index 41d7f0cca..000000000 --- a/workflows/transcriptomics/rnaseq-de/test-data/SRR5085167.tabular +++ /dev/null @@ -1,7128 +0,0 @@ -Geneid SRR5085167 -YDL246C 0 -YDL243C 0 -YDR387C 4 -YDL094C 0 -YDR438W 0 -YDR523C 0 -YDR542W 0 -YDR492W 10 -YDR018C 1 -YDL189W 2 -YDR508C 31 -YDR462W 3 -YDR175C 5 -YDR186C 5 -YDR150W 20 -YDR243C 1 -YDL182W 37 -YDR362C 5 -YDR232W 13 -YDR158W 85 -YDR439W 9 -YDL206W 3 -YDR125C 0 -YDR338C 6 -YDR526C 0 -YDR533C 5 -YDR272W 9 -YDR197W 7 -YDR512C 2 -YDR489W 2 -YDR299W 29 -YDL015C 23 -YDR304C 22 -YDR271C 0 -YDL181W 3 -YDR367W 12 -YDR085C 1 -YDL097C 37 -YDL139C 0 -YDR200C 4 -YDR191W 1 -YDR451C 5 -YDR469W 1 -YDR470C 4 -YDR105C 15 -YDR483W 69 -YDL123W 1 -YDL199C 1 -YDR505C 8 -YDL045W-A 2 -YDL045C 4 -YDR361C 12 -YDR406W-A 0 -YDR199W 0 -YDR266C 16 -YDL242W 0 -YDR002W 52 -YDR214W 12 -YDR130C 1 -YDL176W 3 -YDR358W 2 -YDR544C 0 -YDR460W 1 -snR84 7 -YDR034W-B 0 -YDL028C 3 -YDR061W 7 -YDR060W 53 -YDR169C-A 0 -YDR363W 10 -YDR422C 7 -YDR119W 27 -tR(ACG)D 0 -YDR097C 13 -YDR042C 1 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100644 index dd03db31e..000000000 --- a/workflows/transcriptomics/rnaseq-de/test-data/SRR5085170.tabular +++ /dev/null @@ -1,7128 +0,0 @@ -Geneid SRR5085170 -YDL246C 0 -YDL243C 0 -YDR387C 6 -YDL094C 0 -YDR438W 0 -YDR523C 1 -YDR542W 0 -YDR492W 9 -YDR018C 0 -YDL189W 5 -YDR508C 47 -YDR462W 1 -YDR175C 5 -YDR186C 7 -YDR150W 35 -YDR243C 8 -YDL182W 36 -YDR362C 9 -YDR232W 22 -YDR158W 102 -YDR439W 3 -YDL206W 7 -YDR125C 0 -YDR338C 7 -YDR526C 0 -YDR533C 10 -YDR272W 13 -YDR197W 4 -YDR512C 3 -YDR489W 4 -YDR299W 27 -YDL015C 26 -YDR304C 40 -YDR271C 0 -YDL181W 2 -YDR367W 21 -YDR085C 4 -YDL097C 49 -YDL139C 0 -YDR200C 7 -YDR191W 4 -YDR451C 6 -YDR469W 3 -YDR470C 1 -YDR105C 18 -YDR483W 91 -YDL123W 6 -YDL199C 2 -YDR505C 12 -YDL045W-A 2 -YDL045C 2 -YDR361C 20 -YDR406W-A 0 -YDR199W 0 -YDR266C 16 -YDL242W 0 -YDR002W 72 -YDR214W 23 -YDR130C 4 -YDL176W 11 -YDR358W 2 -YDR544C 0 -YDR460W 15 -snR84 0 -YDR034W-B 0 -YDL028C 7 -YDR061W 6 -YDR060W 68 -YDR169C-A 0 -YDR363W 8 -YDR422C 7 -YDR119W 32 -tR(ACG)D 0 -YDR097C 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