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Co-authored-by: kate-bowers-broad <kbowers@broadinstitute.org>
Co-authored-by: kate-bowers-broad <kbowers@broadinstitute.org>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Co-authored-by: kate-bowers-broad <kbowers@broadinstitute.org>
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@kate-bowers-broad @ErinWeisbart If you merge in the changes from that branch then you should be able get your step working pretty quickly. |
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Aug 21, 2025
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I merged the changes in from the dev branch and hooked up the process you two wrote. You can see the non-merge fixes I made in commit 9ce279f .
I've got some additional comments with next steps to get this PR ready for review. Key points are:
- Fix cppipe file input staging
- Fix nf-test file
- Run nf-test and create snapshots
- (if-minor) consider preserving metadata in output file
| output: | ||
| output: | ||
| tuple val(meta), path("assaydevelopment/*.png"), emit: png | ||
| tuple val(meta), path("assaydevelopment/Image.csv"), emit: csv, optional: true |
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As a continuation of the above comment, can we get this to pick up the file at: ${meta.id}.csv ?
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I changed the .cppipe to output the .csv file as "_ImageQCMeasurements.csv".
I'm not sure how to make that match ${meta.id}
| touch ${prefix}.bam | ||
| mkdir -p assaydevelopment | ||
| echo 'this is not assay development' > assaydevelopment/mock_segmentedimage.png | ||
| echo 'this is not assay development' > assaydevelopment/mock_Image.csv |
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If we change the output file pattern/name we should mirror it here.
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| echo 'this is not assay development' > assaydevelopment/mock_Image.csv | |
| echo 'this is not assay development' > assaydevelopment/${meta.id}.csv |
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This file needs to be updated with the new process format
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In cellpainting/workflows/cellpainting.nf Line 61 in cb7ed70 |
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Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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- assaydevelopment.cppipe from #30 - analysis.cppipe from cpg0000-jump-pilot (CPJUMP1_analysis_without_batchfile) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Very much in draft form at this point.
Outstanding questions:
• Do we want to include logic to support auto-pipeline creation/manipulation based on input channels? (I have some json and python code that I can pull from elsewhere as a starting point if so).
• In
assaydevelopment/main.nfdo the outputs of the illum step need to be moved to the input folder so a single input folder flag can be passed to CellProfiler for file location?• In the
workflows/cellpainting.nfwe were not sure how to properly create theload_data.csv