Add correlation of samples on peaks workflow

workflows/epigenetics/correlation-of-samples-on-peaks/.dockstore.yml

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+version: 1.2
+workflows:
+- name: correlation-of-samples-on-peaks
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /correlation-of-samples-on-peaks.ga
+  testParameterFiles:
+  - /correlation-of-samples-on-peaks-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960
+  - name: Alexandre Mayran
+    orcid: 0000-0002-1228-0308
+  - name: Olusegun E. Adebayo
+    orcid: 0009-0003-9444-3944

workflows/epigenetics/correlation-of-samples-on-peaks/CHANGELOG.md

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+# Changelog
+
+## [0.1] 20206-07-06
+
+First release.

workflows/epigenetics/correlation-of-samples-on-peaks/README.md

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+# correlation of samples on peaks:
+
+## Input datasets
+
+- A collection (list) of peak files.
+- A collection (list) of BAM or CRAM files
+
+## Inputs values
+
+- Reference genome: this field will be adapted to the genomes for bedtools sort (dbkeys table)
+
+## Processing
+
+- The workflow will concatenate the list of peak files given as input
+- Sorts and merges the concatenated BED file by Chromosome using `bedtools sortBED` and `bedtools mergeBED`, respectively.
+- Computes the read coverages for each BAM/CRAM file on the sorted and merged list of genomic region present in the bed files using `multiBamSummary`.
+- Calculate and visualize pairwise correlation values between the read coverages using the tool `plotCorrelation`.
+- The workflow produces three outputs:
+  - a compressed numpy array containing the raw count of the read coverages (i.e., the output of `multiBamSummary`) in .npz format
+  - The same raw count of the read coverages (i.e., the output of `multiBamSummary`) in .tabular format
+  - a plot of pairwise correlation values between the read coverages (i.e., the output of `plotCorrelation`).

workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks-tests.yml

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+- doc: Test outline for correlation-of-samples-on-peaks
+  job:
+    Collection of peak files:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: peak2
+        path: test-data/peak2.bed
+      - class: File
+        identifier: peak1
+        path: test-data/peak1.bed
+    BAM or CRAM files:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: sample2
+        path: test-data/sample2.bam
+      - class: File
+        identifier: sample1
+        path: test-data/sample1.bam
+    Reference genome: mm39
+  outputs:
+    correlation plot:
+      path: test-data/correlation plot.png
+    deeptool raw counts:
+      path: test-data/deeptool raw counts.tabular
+      sort: true
+    deeptools coverage matrix:
+      path: test-data/deeptools coverage matrix.deeptools_coverage_matrix
+      compare: sim_size