From 69c05cad1aaf0c49cecf761620d0ccd161800be7 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 27 Jul 2026 08:43:47 +0000 Subject: [PATCH 1/3] Updating workflows/epigenetics/correlation-of-samples-on-peaks from 0.1 to 0.2 --- .../CHANGELOG.md | 6 +++++ .../correlation-of-samples-on-peaks.ga | 24 +++++++++---------- 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/workflows/epigenetics/correlation-of-samples-on-peaks/CHANGELOG.md b/workflows/epigenetics/correlation-of-samples-on-peaks/CHANGELOG.md index ae100a4390..35da08c5dc 100644 --- a/workflows/epigenetics/correlation-of-samples-on-peaks/CHANGELOG.md +++ b/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 diff --git a/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks.ga b/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks.ga index 14aa0a961c..802600fe6f 100644 --- a/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks.ga +++ b/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" } \ No newline at end of file From 33c0facd8de51bb8e6ca124922ac76cedaf2565b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 3 Aug 2026 10:13:31 +0200 Subject: [PATCH 2/3] use image_diff comparison for png --- .../correlation-of-samples-on-peaks-tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks-tests.yml b/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks-tests.yml index 418aacb2f0..26a3f01a86 100644 --- a/workflows/epigenetics/correlation-of-samples-on-peaks/correlation-of-samples-on-peaks-tests.yml +++ b/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 From 78aa4f00154e6f98afa7b9e6ac878a2fb14f7244 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 3 Aug 2026 10:42:48 +0200 Subject: [PATCH 3/3] Add Segun and myself to CODEOWNERS --- .github/CODEOWNERS | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index b55b8e5087..7f230867c3 100644 --- a/.github/CODEOWNERS +++ b/.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