Add clean version of DESeq2 LRT workflows

Author: michael-kotliar

tools/deseq-lrt-step-1.cwl

@@ -1,288 +1,136 @@
 cwlVersion: v1.0
 class: CommandLineTool
 
-requirements:
-  - class: InlineJavascriptRequirement
-
 hints:
 - class: DockerRequirement
-  dockerPull: "biowardrobe2/scidap-deseq:v0.0.72"
+  dockerPull: biowardrobe2/diff-tools:v0.0.1
 
 inputs:
 
-  dsq_obj_data:
-    type: File?
-    inputBinding:
-      prefix: "--dsq_obj_data"
-    doc: "RDS file containing the contrasts list from step 1"
-
-  contrasts_table:
-    type: File?
+  query_rds:
+    type: File
     inputBinding:
-      prefix: "--contrast_df"
-    doc: "TSV file containing contrasts data"
+      prefix: "--query"
 
-  batchcorrection:
+  target_contrasts:
     type:
-      - "null"
-      - type: enum
-        symbols:
-          - "none"
-          - "combatseq"
-          - "model"
-    inputBinding:
-      prefix: "--batchcorrection"
-    default: "none"
-    doc: "Batch correction method. Default: none"
-
-  contrast_indices:
-    type: string
+    - string
+    - string[]
     inputBinding:
-      prefix: "--contrast_indices"
-    doc: "Comma-separated list of integers representing contrast indices (e.g., 1,2,3)"
+      prefix: "--target"
 
-  fdr_cutoff:
+  padj_threshold:
     type: float?
     inputBinding:
-      prefix: "--fdr"
-    default: 0.1
-    doc: |
-      In the exploratory visualization part of the analysis, output only features with adjusted p-value (FDR) not bigger than this value.
-      Default: 0.1.
+      prefix: "--padj"
 
-  lfcthreshold:
+  logfc_threshold:
     type: float?
     inputBinding:
-      prefix: "--lfcthreshold"
-    default: 0.59
-    doc: |
-      Log2 fold change threshold for determining significant differential expression.
-      Genes with absolute log2 fold change greater than this threshold will be considered.
-      Default: 0.59 (about 1.5 fold change)
+      prefix: "--logfc"
 
-  regulation:
+  alternative_hypothesis:
     type:
-      - "null"
-      - type: enum
-        symbols:
-          - "both"
-          - "up"
-          - "down"
-    inputBinding:
-      prefix: "--regulation"
-    default: "both"
-    doc: |
-      Direction of differential expression comparison. β is the log2 fold change.
-      'both' for both up and downregulated genes (|β| > lfcThreshold);
-      'up' for upregulated genes (β > lfcThreshold);
-      'down' for downregulated genes (β < -lfcThreshold).
-      Default: both
-
-  output_prefix:
-    type: string?
-    inputBinding:
-      prefix: "--output"
-    default: "deseq-lrt-step-2"
-    doc: "Output prefix"
-
-  use_lfc_thresh:
-    type: boolean
+    - "null"
+    - type: enum
+      symbols:
+      - "greater"
+      - "less"
+      - "lessAbs"
+      - "greaterAbs"
     inputBinding:
-      prefix: "--use_lfc_thresh"
-      valueFrom: "$(self ? 'TRUE' : 'FALSE')"
-    default: false
-    doc: "Use lfcthreshold as the null hypothesis value in the results function call. Default: TRUE"
+      prefix: "--alternative"
 
   cluster_method:
     type:
-      - "null"
-      - type: enum
-        symbols:
-          - "row"
-          - "column"
-          - "both"
-          - "none"
+    - "null"
+    - type: enum
+      symbols:
+      - "row"
+      - "column"
+      - "both"
     inputBinding:
       prefix: "--cluster"
-    default: "none"
-    doc: |
-      Hopach clustering method to be run on normalized read counts for the
-      exploratory visualization part of the analysis. Default: do not run
-      clustering
 
-  row_distance:
+  cluster_row_distance:
     type:
-      - "null"
-      - type: enum
-        symbols:
-          - "cosangle"
-          - "abscosangle"
-          - "euclid"
-          - "cor"
-          - "abscor"
+    - "null"
+    - type: enum
+      symbols:
+      - "cosangle"
+      - "abscosangle"
+      - "euclid"
+      - "abseuclid"
+      - "cor"
+      - "abscor"
     inputBinding:
       prefix: "--rowdist"
-    doc: |
-      Distance metric for HOPACH row clustering. Ignored if --cluster is not
-      provided. Default: cosangle
 
-  column_distance:
+  cluster_col_distance:
     type:
-      - "null"
-      - type: enum
-        symbols:
-          - "cosangle"
-          - "abscosangle"
-          - "euclid"
-          - "cor"
-          - "abscor"
+    - "null"
+    - type: enum
+      symbols:
+      - "cosangle"
+      - "abscosangle"
+      - "euclid"
+      - "abseuclid"
+      - "cor"
+      - "abscor"
     inputBinding:
       prefix: "--columndist"
-    doc: |
-      Distance metric for HOPACH column clustering. Ignored if --cluster is not
-      provided. Default: euclid
 
-  scaling_type:
-    type:
-      - "null"
-      - type: enum
-        symbols:
-          - "minmax"
-          - "zscore"
+  cluster_max_depth:
+    type: int?
     inputBinding:
-      prefix: "--scaling_type"
-    default: "zscore"
-    doc: |
-      Specifies the type of scaling to be applied to the expression data.
-      'minmax' applies Min-Max scaling, normalizing values to a range of [-2, 2].
-      'zscore' applies Z-score standardization, centering data to mean = 0 and standard deviation = 1.
-      Default: none (no scaling applied).
-      **Note:** If 'minmax' or 'zscore' is selected, all genes/features will be scaled accordingly before further analysis.
+      prefix: "--depth"
 
-  k_hopach:
+  cluster_max_branches:
     type: int?
     inputBinding:
-      prefix: "--k"
-    default: 3
-    doc: "Number of levels (depth) for Hopach clustering: min - 1, max - 15. Default: 3."
+      prefix: "--branches"
 
-  kmax_hopach:
-    type: int?
+  output_prefix:
+    type: string?
     inputBinding:
-      prefix: "--kmax"
-    default: 5
-    doc: "Maximum number of clusters at each level for Hopach clustering: min - 2, max - 9. Default: 5."
+      prefix: "--output"
 
   threads:
     type: int?
     inputBinding:
-      prefix: "--threads"
-    default: 1
-    doc: "Number of threads"
-
-  test_mode:
-    type: boolean
-    inputBinding:
-      prefix: "--test_mode"
-      valueFrom: "$(self ? 'TRUE' : 'FALSE')"
-    default: false
-    doc: "Run for test, only first 100 rows"
+      prefix: "--cpus"
 
 outputs:
 
-  diff_expr_files:
-    type: File[]
+  vlcn_png:
+    type:
+    - "null"
+    - type: array
+      items: File
     outputBinding:
-      glob: "*_gene_exp_table.tsv"
+      glob: "*_vlcn.png"
 
-  mds_plots_html:
-    type: File
+  read_counts_gct:
+    type: File?
     outputBinding:
-      glob: "mds_plot.html"
+      glob: "*_read_counts.gct"
 
-  counts_all_gct:
-    type: File
+  read_counts_html:
+    type: File?
     outputBinding:
-      glob: "counts_all.gct"
+      glob: "*_read_counts.html"
 
-  counts_filtered_gct:
+  diff_expr_tsv:
     type: File
     outputBinding:
-      glob: "counts_filtered.gct"
+      glob: "*_diff_expr.tsv"
 
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
-baseCommand: ["/usr/bin/Rscript", "/usr/local/bin/run_deseq_lrt_step_2.R"]
-stdout: deseq_lrt_step_2_stdout.log
-stderr: deseq_lrt_step_2_stderr.log
-
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-  - https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
-
-s:name: "DESeq2 (LRT Step 2) - Differential gene expression analysis using contrasts"
-label: "DESeq2 (LRT Step 2) - Differential gene expression analysis using contrasts"
-s:alternateName: "Differential gene expression analysis using DESeq2 contrasts"
-
-s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/deseq-lrt-step-2.cwl
-s:codeRepository: https://github.com/Barski-lab/workflows
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-  - class: s:Organization
-    s:legalName: "Cincinnati Children's Hospital Medical Center"
-    s:location:
-      - class: s:PostalAddress
-        s:addressCountry: "USA"
-        s:addressLocality: "Cincinnati"
-        s:addressRegion: "OH"
-        s:postalCode: "45229"
-        s:streetAddress: "3333 Burnet Ave"
-        s:telephone: "+1(513)636-4200"
-    s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-    s:department:
-      - class: s:Organization
-        s:legalName: "Allergy and Immunology"
-        s:department:
-          - class: s:Organization
-            s:legalName: "Barski Research Lab"
-            s:member:
-              - class: s:Person
-                s:name: Michael Kotliar
-                s:email: mailto:[email protected]
-                s:sameAs:
-                  - id: http://orcid.org/0000-0002-6486-3898
-
-doc: |
-  Runs DESeq2 analysis using contrasts from previous LRT step.
-
-  This tool takes the outputs from DESeq2 LRT step 1 and performs differential expression analysis using specified contrasts.
-
-  **Inputs:**
-
-  - `expression_data_rds`: RDS file containing the expression data from step 1.
-  - `contrasts_rds`: RDS file containing the contrasts list from step 1.
-  - `dsq_wald_rds`: RDS file containing the DESeq2 object from the Wald test in step 1.
-  - `metadata_rds`: RDS file containing the metadata from step 1.
-  - `contrast_indices`: Comma-separated list of integers representing contrast indices (e.g., 1,2,3).
-  - `fdr`: Adjusted p-value (FDR) threshold for significance. Default: 0.1.
-  - `lfcthreshold`: Log2 fold change threshold for significance. Default: 0.59.
-  - `regulation`: Direction of differential expression comparison ('both', 'up', 'down'). Default: 'both'.
-
-  **Outputs:**
-
-  - Differential expression reports for each contrast.
-  - MA plots (PNG and PDF) for each contrast.
-  - MDS plots (HTML) for each contrast.
-  - GCT files (counts_all.gct and counts_filtered.gct) for each contrast.
+baseCommand: [run_deseq_lrt_step_2.sh]
+stdout: error_msg.txt
+stderr: error_report.txt