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Wrap process invocations in conditionals #141

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Wrap process invocations in conditionals #141

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0dc6b79
fix(segmentation): wrap process invocations in conditionals for AWS B…
adamjtaylor Feb 3, 2026
8f3c844
fix(mccellpose): add pixel size argument for MCCELLPOSE process
adamjtaylor Feb 3, 2026
9a3e628
fix(cellpose): refactor channel handling for cellpose segmentation pr…
adamjtaylor Feb 3, 2026
1454694
fix(cellpose): update model input to allow optional model path
adamjtaylor Feb 4, 2026
90b092b
fix(cellpose): update model input to use stageAs for optional model path
adamjtaylor Feb 4, 2026
a15c5a9
fix(cellpose, deepcell): add 'process_gpu' label to CELLPOSE and DEEP…
adamjtaylor Feb 4, 2026
760ff66
fix(cellpose): add 'channel_axis' argument to CELLPOSE process
adamjtaylor Feb 5, 2026
876427a
fix(cellpose): update CELLPOSE arguments to use '--channel_axis' format
adamjtaylor Feb 5, 2026
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2 changes: 2 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ process {
}

withName: "CELLPOSE" {
ext.args = {"--channel_axis 0"}
ext.when = {params.segmentation && params.segmentation.split(',').contains('cellpose')}
publishDir = [
path: { "${params.outdir}/segmentation/cellpose" },
Expand All @@ -82,6 +83,7 @@ process {
}

withName: "MCCELLPOSE" {
ext.args = { "--pixel-size=${meta.pixel_size}" }
ext.when = {params.segmentation && params.segmentation.split(',').contains('mccellpose')}
publishDir = [
path: { "${params.outdir}/segmentation/mccellpose" },
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3 changes: 2 additions & 1 deletion modules/nf-core/cellpose/main.nf
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1 change: 1 addition & 0 deletions modules/nf-core/deepcell/mesmer/main.nf
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56 changes: 33 additions & 23 deletions workflows/mcmicro.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -126,34 +126,44 @@ workflow MCMICRO {
}

// Run Segmentation
// Each segmenter is conditionally invoked based on params.segmentation to avoid
// input validation errors on AWS Batch when the process would be skipped by ext.when

ch_masks = channel.empty()

ch_segmentation_input
.multiMap{ meta, image ->
img: [meta + [segmenter: 'mesmer'], image]
membrane_img: [[:], []]
}
| DEEPCELL_MESMER
ch_masks = ch_masks.mix(DEEPCELL_MESMER.out.mask)
ch_versions = ch_versions.mix(DEEPCELL_MESMER.out.versions)
if (params.segmentation?.split(',')?.contains('mesmer')) {
ch_segmentation_input
.multiMap{ meta, image ->
img: [meta + [segmenter: 'mesmer'], image]
membrane_img: [[:], []]
}
| DEEPCELL_MESMER
ch_masks = ch_masks.mix(DEEPCELL_MESMER.out.mask)
ch_versions = ch_versions.mix(DEEPCELL_MESMER.out.versions)
}

ch_segmentation_input
.multiMap{ meta, image ->
image: [meta + [segmenter: 'cellpose'], image]
model: params.cellpose_model
}
| CELLPOSE
ch_masks = ch_masks.mix(CELLPOSE.out.mask)
ch_versions = ch_versions.mix(CELLPOSE.out.versions)
if (params.segmentation?.split(',')?.contains('cellpose')) {
ch_cellpose_image = ch_segmentation_input
.map{ meta, image -> [meta + [segmenter: 'cellpose'], image] }

ch_segmentation_input
.multiMap{ meta, image ->
image: [meta + [segmenter: 'mccellpose'], image]
}
| MCCELLPOSE
ch_masks = ch_masks.mix(MCCELLPOSE.out.mask)
ch_versions = ch_versions.mix(MCCELLPOSE.out.versions)
ch_cellpose_model = params.cellpose_model
? Channel.fromPath(params.cellpose_model, checkIfExists: true)
: Channel.value([])

CELLPOSE(ch_cellpose_image, ch_cellpose_model)
ch_masks = ch_masks.mix(CELLPOSE.out.mask)
ch_versions = ch_versions.mix(CELLPOSE.out.versions)
}

if (params.segmentation?.split(',')?.contains('mccellpose')) {
ch_segmentation_input
.multiMap{ meta, image ->
image: [meta + [segmenter: 'mccellpose'], image]
}
| MCCELLPOSE
ch_masks = ch_masks.mix(MCCELLPOSE.out.mask)
ch_versions = ch_versions.mix(MCCELLPOSE.out.versions)
}

// Run Quantification

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