Merge pull request #573 from dianichj/pseudo-bulk-edger-workflow

Add files for pseudobulk workflow using decoupler and edgeR

workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /pseudo-bulk_edgeR.ga
+  testParameterFiles:
+  - /pseudo-bulk_edgeR-tests.yml
+  authors:
+  - name: Diana Chiang Jurado
+    orcid: 0000-0002-5857-1477
+  - name: Pavankumar Videm
+    orcid: 0000-0002-5192-126X
+  - name: Pablo Moreno
+    orcid: 0000-0002-9856-1679

workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-10-14
+First release.

workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/README.md

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+# Pseudobulk-edgeR workflows
+
+This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated 
+using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG 
+analysis.
+
+## Inputs
+
+- deCoupler: Source AnnData (`h5ad`).
+    - Parameter: Pseudobulk: Fields to merge / optional 
+    - Parameter: Group by column / has to be given
+    - Parameter: Sample key column / has to be given
+    - Parameter: Name your raw count layer / has to be given
+    - Parameter: Factor Field / has to be given
+- edgeR:
+    - Sanitzed Count Matrix
+    - Sanitized Factor File
+    - Cleaned Gene Annotations file
+    - Parameter: Formula for linear model / has to be given
+    - Contrast file / has to be given
+- Volcano Plot:
+    - Input (`tabular`) file with genesymbol, logFC, Pvalue and FDR columns.
+
+## Processing
+
+Sanitzation steps after decoupler:
+- Sanitize Matrix and Factors(`tabular`): finds [ --+*^]+ and replace with -
+- Remove start, end with (`tabular`): A column that may affect EdgeR and DESeq2.
+- Sanitize First Factor for leading digits (`tabular`): Finds ^([0-9])(.+) and replace it with GG_\\1\\2
+- Get Contrast labels
+- Replace text
+- Split Contrasts
+- Contrasts as Parameters: Plot title
+- Select columns for volcano plot using (`Remove columns`) from DEG edgeR (`Table`)output.
+
+
+## Outputs
+
+  - Pseudobulk_count_matrix (`tabular`)
+  - Pseudobulk Plot (`png`)
+  - Filtered by expression (`png`)
+  - Table DEG
+  - Results (`HTML`) File and plots for download within the output as (`png`)
+  - Volcano plot (`PDF`)

workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR-tests.yml

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+- doc: Test outline for pseudo-bulk_edgeR
+  job:
+    Source AnnData file:
+      class: File
+      location: https://zenodo.org/records/13929549/files/Source%20AnnData%20file.h5ad
+      filetype: h5ad
+    'Pseudo-bulk: Fields to merge': null
+    Group by column: cell_type
+    Sample key column: individual
+    Name Your Raw Counts Layer: counts
+    Factor fields: disease
+    Gene symbol column: gene_symbol
+    Formula: '~ 0 + disease'
+  outputs:
+    'Pseudobulk count matrix':
+        has_text_matching:
+          expression: "ACAP2\t9.0\t18.0\t20.0\t68.0\t106.0\t122.0\t14.0\t259.0\t279.0\t184.0\t612.0\t293.0\t297.0\t46.0\t1.0\t0.0\t1.0\t12.0\t229.0\t151.0\t141.0\t309.0\t299.0\t181.0\t2.0\t2.0\t28.0\t15.0\t54.0\t210.0\t1.0\t1.0\t1.0\t11.0"
+          expression: "ACER3\t4.0\t25.0\t21.0\t110.0\t82.0\t91.0\t22.0\t326.0\t297.0\t211.0\t1004.0\t574.0\t370.0\t108.0\t0.0\t0.0\t2.0\t2.0\t188.0\t113.0\t135.0\t322.0\t324.0\t159.0\t7.0\t7.0\t32.0\t5.0\t33.0\t89.0\t2.0\t2.0\t8.0\t48.0"
+    'Pseudobulk Plot':
+      element_test:
+        has_size: 40116
+        delta: 2000 
+    'Filtered by expression':
+      element_test:
+        has_size: 23490
+        delta: 2000 
+    'Report Results: HTML File':
+      element_test:
+        has_size: 531761
+        delta: 25000
+    'Tables: DEG':
+      element_tests:
+        edgeR_normal-COVID_19:
+          has_text_matching:
+            expression: "RALBP1\tENSG00000017797\tFalse\t0.518[0-9]*\t1.609[0-9]*\t0.402[0-9]*\t2\tFalse\t0.286[0-9]*\t0.552[0-9]*\t-1.967[0-9]*\t7.483[0-9]*\t12.0213[0-9]*\t0.001[0-9]*\t0.436[0-9]*"
+            expression: "NAPA\tENSG00000105402\tTrue\t0.342[0-9]\t1.686[0-9]\t0.846[0-9]\t4\tFalse\t0.180[0-9]\t0.440[0-9]\t-1.059[0-9]\t6.833[0-9]\t3.291[0-9]\t0.076[0-9]\t0.619[0-9]"
+          has_n_lines:
+            n: 1430
+            delta: 1
+    'Tables for volcano plot':
+      element_tests:
+        edgeR_normal-COVID_19:
+          has_text_matching:
+            expression: "CPEB4\t-2.402[0-9]\t0.001[0-9]\t0.436[0-9]"
+            expression: "FGFR1OP2\t-2.367[0-9]\t0.004[0-9]\t0.458[0-9]"
+    'Volcano Plot on input dataset(s): PDF':
+      element_tests:
+        edgeR_normal-COVID_19:
+          has_size: 85052
+          delta: 2000