Add correlation of samples on peaks workflow

[OEAdebayo]

new galaxy workflow correlation-of-samples-on-peaks

[lldelisle]

Thanks @OEAdebayo for putting this workflow on IWC. I added suggestions to the README. Please if you modify your README, think about modifying also the README in the .ga file.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

• ✅ correlation-of-samples-on-peaks.ga_0

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Collection of peak files:

      • step_state: scheduled

    • Step 2: Reference genome:

      • step_state: scheduled

    • Step 3: BAM or CRAM files:

      • step_state: scheduled

    • Step 4: Concatenate all files into one (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/coreutils:9.5

          Command Line:

          • cat '/tmp/tmpvhzh18uw/files/e/c/b/dataset_ecb1b7c5-025e-45d1-b216-99d4eb31654d.dat' >> '/tmp/tmpvhzh18uw/job_working_directory/000/5/outputs/dataset_61e07a71-534d-402b-99f8-ac4b46b8213a.dat' && cat '/tmp/tmpvhzh18uw/files/c/d/2/dataset_cd2f8f0a-524c-4444-8d18-3251c4e575c8.dat' >> '/tmp/tmpvhzh18uw/job_working_directory/000/5/outputs/dataset_61e07a71-534d-402b-99f8-ac4b46b8213a.dat' && exit 0

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3ebecd0808411f18d846045bd0775cc"
            chromInfo	"/tmp/tmpvhzh18uw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 5: Sort bed files (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • sortBed -i '/tmp/tmpvhzh18uw/files/6/1/e/dataset_61e07a71-534d-402b-99f8-ac4b46b8213a.dat'   -g '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm39.len'  > '/tmp/tmpvhzh18uw/job_working_directory/000/6/outputs/dataset_50d11dbf-cb95-40e7-a3c5-02cb22d9c287.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3ebecd0808411f18d846045bd0775cc"
            chromInfo	"/tmp/tmpvhzh18uw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            genome_file_opts	{"__current_case__": 0, "genome": "mm39", "genome_file_opts_selector": "loc"}
            option	""

    • Step 6: Merge bed file (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • mergeBed -i '/tmp/tmpvhzh18uw/files/5/0/d/dataset_50d11dbf-cb95-40e7-a3c5-02cb22d9c287.dat'  -d 0    > '/tmp/tmpvhzh18uw/job_working_directory/000/7/outputs/dataset_a4a4de61-6934-4317-839a-ca02b30a6b26.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3ebecd0808411f18d846045bd0775cc"
            c_and_o_argument_repeat	[]
            chromInfo	"/tmp/tmpvhzh18uw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            distance	"0"
            header	false
            strand	""

    • Step 7: multiBam summary (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0

          Command Line:

          • ln -s '/tmp/tmpvhzh18uw/files/2/0/5/dataset_205f2b76-5dd5-4497-a7c2-b7b99f91fce7.dat' './0.bam' && ln -s '/tmp/tmpvhzh18uw/files/_metadata_files/d/d/a/metadata_dda3e82d-a71e-41c8-adbe-f4ab70725d75.dat' './0.bam.bai' && ln -s '/tmp/tmpvhzh18uw/files/f/e/1/dataset_fe1d4346-a1ef-4751-bb72-25effb1d9dfc.dat' './1.bam' && ln -s '/tmp/tmpvhzh18uw/files/_metadata_files/e/5/0/metadata_e50c09aa-e9a7-4393-b26c-a7a093721064.dat' './1.bam.bai' &&   multiBamSummary BED-file --numberOfProcessors "${GALAXY_SLOTS:-4}"  --outFileName '/tmp/tmpvhzh18uw/job_working_directory/000/8/outputs/dataset_58f9c74c-3576-4a69-a989-9c43b23c08ea.dat' --bamfiles '0.bam' '1.bam' --labels 'sample2' 'sample1'  --outRawCounts '/tmp/tmpvhzh18uw/job_working_directory/000/8/outputs/dataset_bcdb867e-a6b8-4dbc-aa1f-ba787be24aa8.dat'   --BED /tmp/tmpvhzh18uw/files/a/4/a/dataset_a4a4de61-6934-4317-839a-ca02b30a6b26.dat

          Exit Code:

          • 0

          Standard Error:

          • Number of bins found: 20
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3ebecd0808411f18d846045bd0775cc"
            advancedOpt	{"__current_case__": 0, "showAdvancedOpt": "no"}
            chromInfo	"/tmp/tmpvhzh18uw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            custom_sample_labels_conditional	{"__current_case__": 0, "custom_labels_select": "No"}
            dbkey	"?"
            mode	{"__current_case__": 1, "modeOpt": "BED-file", "region_file": {"values": [{"id": 7, "src": "hda"}]}}
            multibam_conditional	{"__current_case__": 0, "bamfiles": {"values": [{"id": 2, "src": "hdca"}]}, "orderMatters": "No"}
            outRawCounts	true
            region	""
            scalingFactors	false

    • Step 8: Plot correlation (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0

          Command Line:

          • plotCorrelation --corData '/tmp/tmpvhzh18uw/files/5/8/f/dataset_58f9c74c-3576-4a69-a989-9c43b23c08ea.dat' --plotFile '/tmp/tmpvhzh18uw/job_working_directory/000/9/outputs/dataset_3530fe0a-4945-4a43-bb94-0b1dce4281a7.dat' --corMethod 'spearman' --whatToPlot 'heatmap'  --colorMap 'RdYlBu' --plotNumbers --plotTitle ''  --plotWidth 11.0 --plotHeight 9.5  --plotFileFormat 'png'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3ebecd0808411f18d846045bd0775cc"
            chromInfo	"/tmp/tmpvhzh18uw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            corMethod	"spearman"
            dbkey	"?"
            outFileCorMatrix	false
            outFileFormat	"png"
            plotting_type	{"__current_case__": 0, "colorMap": "RdYlBu", "plotHeight": "9.5", "plotNumbers": true, "plotTitle": "", "plotWidth": "11.0", "whatToPlot": "heatmap", "zMax": "", "zMin": ""}
            removeOutliers	false
            skipZeros	false

  • Other invocation details

    • history_id

      • bce96b1d9a8251c8

    • history_state

      • ok

    • invocation_id

      • bce96b1d9a8251c8

    • invocation_state

      • scheduled

    • workflow_id

      • bce96b1d9a8251c8

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

• ✅ correlation-of-samples-on-peaks.ga_0

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Collection of peak files:

      • step_state: scheduled

    • Step 2: Reference genome:

      • step_state: scheduled

    • Step 3: BAM or CRAM files:

      • step_state: scheduled

    • Step 4: Concatenate all files into one (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/coreutils:9.5

          Command Line:

          • cat '/tmp/tmp0x9tlcvl/files/c/6/d/dataset_c6df213c-f3b7-47e5-b023-b1a4bbb55dfb.dat' >> '/tmp/tmp0x9tlcvl/job_working_directory/000/5/outputs/dataset_09c1fd45-282b-4076-acd2-cd5b725203fd.dat' && cat '/tmp/tmp0x9tlcvl/files/8/a/6/dataset_8a6fce7a-7fa7-47d3-a658-03228213d9e0.dat' >> '/tmp/tmp0x9tlcvl/job_working_directory/000/5/outputs/dataset_09c1fd45-282b-4076-acd2-cd5b725203fd.dat' && exit 0

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9af4f86a808f11f18d847ced8d550730"
            chromInfo	"/tmp/tmp0x9tlcvl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 5: Sort bed files (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • sortBed -i '/tmp/tmp0x9tlcvl/files/0/9/c/dataset_09c1fd45-282b-4076-acd2-cd5b725203fd.dat'   -g '/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm39.len'  > '/tmp/tmp0x9tlcvl/job_working_directory/000/6/outputs/dataset_f056a1e8-3b95-4395-94ed-d341fce7c659.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9af4f86a808f11f18d847ced8d550730"
            chromInfo	"/tmp/tmp0x9tlcvl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            genome_file_opts	{"__current_case__": 0, "genome": "mm39", "genome_file_opts_selector": "loc"}
            option	""

    • Step 6: Merge bed file (toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bedtools:2.31.1--h13024bc_3

          Command Line:

          • mergeBed -i '/tmp/tmp0x9tlcvl/files/f/0/5/dataset_f056a1e8-3b95-4395-94ed-d341fce7c659.dat'  -d 0    > '/tmp/tmp0x9tlcvl/job_working_directory/000/7/outputs/dataset_fee0ef33-8329-4389-b788-3b67b562a3ab.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9af4f86a808f11f18d847ced8d550730"
            c_and_o_argument_repeat	[]
            chromInfo	"/tmp/tmp0x9tlcvl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            distance	"0"
            header	false
            strand	""

    • Step 7: multiBam summary (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.2+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0

          Command Line:

          • ln -s '/tmp/tmp0x9tlcvl/files/6/d/2/dataset_6d27f5ac-33e9-4421-a998-b7fe87b66a41.dat' './0.bam' && ln -s '/tmp/tmp0x9tlcvl/files/_metadata_files/6/1/6/metadata_6163a9d6-19a1-4fa7-9be7-a452a811c46b.dat' './0.bam.bai' && ln -s '/tmp/tmp0x9tlcvl/files/1/2/1/dataset_12193186-197b-44cb-a927-6d79687c74a8.dat' './1.bam' && ln -s '/tmp/tmp0x9tlcvl/files/_metadata_files/2/a/e/metadata_2ae42507-d33e-43c5-8d44-343fd38a76cc.dat' './1.bam.bai' &&   multiBamSummary BED-file --numberOfProcessors "${GALAXY_SLOTS:-4}"  --outFileName '/tmp/tmp0x9tlcvl/job_working_directory/000/8/outputs/dataset_13aa6e29-a046-43ce-b002-d141dbc29636.dat' --bamfiles '0.bam' '1.bam' --labels 'sample2' 'sample1'  --outRawCounts '/tmp/tmp0x9tlcvl/job_working_directory/000/8/outputs/dataset_ba669909-ba6d-40a6-a2cb-8f4e5e9421a3.dat'   --BED /tmp/tmp0x9tlcvl/files/f/e/e/dataset_fee0ef33-8329-4389-b788-3b67b562a3ab.dat

          Exit Code:

          • 0

          Standard Error:

          • Number of bins found: 20
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9af4f86a808f11f18d847ced8d550730"
            advancedOpt	{"__current_case__": 0, "showAdvancedOpt": "no"}
            chromInfo	"/tmp/tmp0x9tlcvl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            custom_sample_labels_conditional	{"__current_case__": 0, "custom_labels_select": "No"}
            dbkey	"?"
            mode	{"__current_case__": 1, "modeOpt": "BED-file", "region_file": {"values": [{"id": 7, "src": "hda"}]}}
            multibam_conditional	{"__current_case__": 0, "bamfiles": {"values": [{"id": 2, "src": "hdca"}]}, "orderMatters": "No"}
            outRawCounts	true
            region	""
            scalingFactors	false

    • Step 8: Plot correlation (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.2+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0

          Command Line:

          • plotCorrelation --corData '/tmp/tmp0x9tlcvl/files/1/3/a/dataset_13aa6e29-a046-43ce-b002-d141dbc29636.dat' --plotFile '/tmp/tmp0x9tlcvl/job_working_directory/000/9/outputs/dataset_0855bf79-1cfc-469d-9079-bdbbb68acf9b.dat' --corMethod 'spearman' --whatToPlot 'heatmap'  --colorMap 'RdYlBu' --plotNumbers --plotTitle ''  --plotWidth 11.0 --plotHeight 9.5  --plotFileFormat 'png'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9af4f86a808f11f18d847ced8d550730"
            chromInfo	"/tmp/tmp0x9tlcvl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            corMethod	"spearman"
            dbkey	"?"
            outFileCorMatrix	false
            outFileFormat	"png"
            plotting_type	{"__current_case__": 0, "colorMap": "RdYlBu", "plotHeight": "9.5", "plotNumbers": true, "plotTitle": "", "plotWidth": "11.0", "whatToPlot": "heatmap", "zMax": "", "zMin": ""}
            removeOutliers	false
            skipZeros	false

  • Other invocation details

    • history_id

      • 09ba2baa62c5c7bc

    • history_state

      • ok

    • invocation_id

      • 09ba2baa62c5c7bc

    • invocation_state

      • scheduled

    • workflow_id

      • 09ba2baa62c5c7bc

[OEAdebayo]

Fixed the lint error invalid YAML version in .dockstore.yml error.

[lldelisle]

@mvdbeek Do you want to review?

[lldelisle]

Ah I forgot the CODEOWNERS. @mvdbeek how does it works for new members?

[mvdbeek]

Thanks a lot for this contribution, @OEAdebayo! The workflow design is solid — inputs come in as collections, the genome is exposed as a parameter rather than pinned, and the test file is set up correctly with output labels that match the workflow. The comments below are all small fixes; nothing structural.

(Review assembled with Claude Code on my behalf, checked against the IWC reviewer checklist.)

Needs fixing

1. Annotation phrasing

The checklist asks that the annotation start with This workflow does/runs/performs … to generate/analyze/…. Currently it starts with "Takes a list of peak files…". Something like:

This workflow computes read coverage of BAM/CRAM samples over a merged set of peak regions to generate a pairwise correlation plot between samples.

(There's also a double space in "sorts and merges".)

2. Changelog date is malformed

## [0.1] 20206-07-06     ->   ## [0.1] - 2026-07-06

Note the 20206, and the missing - separator that the rest of the repo uses (compare workflows/epigenetics/chipseq-pe/CHANGELOG.md). There are also some trailing-whitespace lines and no newline at end of file.

3. Output label typo

deeptool raw counts should be deepTools raw counts — "deeptool" is a typo for the tool suite name. Please make the same edit in correlation-of-samples-on-peaks-tests.yml so the labels stay in sync. Capitalising the other two labels (Correlation plot, deepTools coverage matrix) would read a bit better too, same sync caveat.

4. Step labels and annotations

• Step 2 annotation: "This takes the BAM /CRAM formated peak files " — "formated" -> "formatted", stray space in "BAM /CRAM", and these are alignment files rather than peak files. Trailing space can go as well.
• Step 3 annotation: "This step concatenate multiple datasets" -> "concatenates".
• Step 6 label: multiBam summary -> multiBamSummary (the actual tool name).
• Steps 6 and 7 have no annotation while every other step does — worth filling in.

5. README

The content covers inputs, the parameter, processing, and all three outputs, which is what we want. Small things:

• Title # correlation of samples on peaks: -> # Correlation of samples on peaks (title case, no trailing colon).
• "Inputs values" -> "Input values".
• workflows/epigenetics/consensus-peaks/ already merges peaks across samples. The checklist asks that a README explain how it differs from a similar existing workflow — a sentence on when to prefer this one (correlation QC across samples) would help users pick.

Passing

• .dockstore.yml: present, valid, and all three authors carry ORCIDs matching the creator block in the .ga exactly.
• Folder name: correlation-of-samples-on-peaks — lowercase, dashes, reads correctly.
• Input/output labels: human readable, no underscores, and all three workflow_outputs labels match the test file.
• Large files: largest test file is 38 KB, so no Zenodo upload needed.

Happy to re-review once these are addressed — thanks again!

[mvdbeek]

You can already add anyone to the CODEOWNERS, and then we add @OEAdebayo as a maintainer.