Updating workflows/epigenetics/correlation-of-samples-on-peaks from 0.1 to 0.2

.github/CODEOWNERS

@@ -46,6 +46,7 @@
 /workflows/epigenetics/consensus-peaks/                                @lldelisle
 /workflows/epigenetics/cutandrun/                                      @lldelisle
 /workflows/epigenetics/hic-hicup-cooler/                               @lldelisle
+/workflows/epigenetics/correlation-of-samples-on-peaks                 @lldelisle @OEAdebayo
 
 # --- genome-assembly ---
 /workflows/genome-assembly/assembly-with-flye/                         @AnnaSyme

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

@@ -1,4 +1,10 @@
 # Changelog
+
+## [0.2] - 2026-07-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0`
 
 ## [0.1] - 2026-07-06
 

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

@@ -24,6 +24,7 @@
   outputs:
     Correlation plot:
       path: test-data/correlation plot.png
+      compare: image_diff
     deepTools raw counts:
       path: test-data/deeptool raw counts.tabular
       sort: true

workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks.ga

@@ -21,7 +21,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release":"0.1",
     "name": "correlation of samples on peaks",
     "readme": "# Correlation of samples on peaks\n\n## Input datasets\n\n- A collection (list) of peak files.\n- A collection (list) of BAM or CRAM files\n\n## Input values\n\n- Reference genome: this field will be adapted to the genomes for bedtools sort (dbkeys table)\n\n## Processing\n\n- The workflow will concatenate the list of peak files given as input\n- Sorts and merges the concatenated BED file by Chromosome using `bedtools sortBED` and `bedtools mergeBED`, respectively.\n- 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`.\n- Calculate and visualize pairwise correlation values between the read coverages using the tool `plotCorrelation`.\n- The workflow produces three outputs:\n  - a compressed numpy array containing the raw count of the read coverages (i.e., the output of `multiBamSummary`) in .npz format\n  - The same raw count of the read coverages (i.e., the output of `multiBamSummary`) in .tabular format\n  - a plot of pairwise correlation values between the read coverages (i.e., the output of `plotCorrelation`).\n\n## Note\n\n A similar workflow `consensus-peaks` creates peaks from raw replicate BAMs via MACS2-based calling and reproducibility filtering while `correlation-of-samples-on-peaks` takes existing peaks together with BAM/CRAM files and tells you how correlated the samples' signal is over those regions. In other words, this workflow serves as a downstream QC step of `consensus-peaks` rather than a peak-calling step itself.",
     "report": {
@@ -90,7 +89,7 @@
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "This takes the BAM/CRAM formated alignment files",
+                    "description": "This takes the BAM/CRAM formatted alignment files",
                     "name": "BAM or CRAM files"
                 }
             ],
@@ -258,7 +257,7 @@
         },
         "6": {
             "annotation": "Computes average read coverage by counting reads from the input BAM/CRAM files over the regions defined in the sorted BED file.",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -298,16 +297,16 @@
                 "top": 1.3972221596870895
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "1fcb7adc39b8",
+                "changeset_revision": "01fb6a7654e6",
                 "name": "deeptools_multi_bam_summary",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"__input_ext\": \"input\", \"advancedOpt\": {\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/data/galaxy/galaxy/var/tool-data/mm10_UCSC/len/mm10_UCSC.len\", \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"modeOpt\": \"BED-file\", \"__current_case__\": 1, \"region_file\": {\"__class__\": \"ConnectedValue\"}}, \"multibam_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bamfiles\": {\"__class__\": \"ConnectedValue\"}}, \"outRawCounts\": true, \"region\": \"\", \"scalingFactors\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "3.5.2+galaxy0",
+            "tool_version": "3.5.4+galaxy0",
             "type": "tool",
             "uuid": "6486b3e8-5e36-4678-970e-f65cd3213f36",
             "when": null,
@@ -326,7 +325,7 @@
         },
         "7": {
             "annotation": "Calculates pairwise correlations between samples using the coverage matrix generated by multiBamSummary",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -349,16 +348,16 @@
                 "top": 5.764769589732765
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.4+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "2c66e43f1c86",
+                "changeset_revision": "bad3ca889618",
                 "name": "deeptools_plot_correlation",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"corData\": {\"__class__\": \"ConnectedValue\"}, \"corMethod\": \"spearman\", \"outFileCorMatrix\": false, \"outFileFormat\": \"png\", \"plotting_type\": {\"whatToPlot\": \"heatmap\", \"__current_case__\": 0, \"zMin\": \"\", \"zMax\": \"\", \"colorMap\": \"RdYlBu\", \"plotTitle\": \"\", \"plotNumbers\": true, \"plotHeight\": \"9.5\", \"plotWidth\": \"11.0\"}, \"removeOutliers\": false, \"skipZeros\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "3.5.2+galaxy0",
+            "tool_version": "3.5.4+galaxy0",
             "type": "tool",
             "uuid": "43017614-cf22-453a-830c-098c2e3d0e4d",
             "when": null,
@@ -372,6 +371,7 @@
         }
     },
     "tags": [],
-    "uuid": "82eb76a0-004f-4780-9e38-868d13d66b6c",
-    "version": 35
+    "uuid": "77911e10-7297-4a6e-a2e8-b41af08bc717",
+    "version": 1,
+    "release": "0.2"
 }