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Merge pull request #47 from RobJY/multi_seg
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Added multiple sequencing methods
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@jmuhlich
jmuhlich authored Jul 19, 2024
2 parents db9f6e8 + 9d187b3 commit cc4a219
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Showing 11 changed files with 270 additions and 30 deletions.
11 changes: 10 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -47,15 +47,24 @@ process {
withName: "DEEPCELL_MESMER" {
ext.prefix = { "mask_${meta.id}" }
ext.args = '--image-mpp=0.215 --nuclear-channel 0 --compartment nuclear'
ext.when = {params.segmentation && params.segmentation.split(',').contains('mesmer')}
publishDir = [
path: { "${params.outdir}/segmentation/deepcell_mesmer" },
mode: params.publish_dir_mode,
]
}

withName: "CELLPOSE" {
ext.when = {params.segmentation && params.segmentation.split(',').contains('cellpose')}
publishDir = [
path: { "${params.outdir}/segmentation/cellpose" },
mode: params.publish_dir_mode,
]
}

withName: MCQUANT {
publishDir = [
path: { "${params.outdir}/quantification/mcquant" },
path: { "${params.outdir}/quantification/mcquant/${meta2.segmenter}" },
mode: params.publish_dir_mode,
]
}
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6 changes: 6 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,12 @@
"cellpose": {
"branch": "master",
"git_sha": "716ef3019b66772a817b417078edce2f7b337858",
"installed_by": ["modules"],
"patch": "modules/nf-core/cellpose/cellpose.diff"
},
"coreograph": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"deepcell/mesmer": {
Expand Down
15 changes: 15 additions & 0 deletions modules/nf-core/cellpose/cellpose.diff
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3 changes: 3 additions & 0 deletions modules/nf-core/cellpose/main.nf
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2 changes: 2 additions & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ params {
input_sample = null
input_cycle = null
marker_sheet = null
segmentation = 'mesmer'
cellpose_model = []

// Illumination correction
illumination = null
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9 changes: 9 additions & 0 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,15 @@
"type": "string",
"enum": ["basicpy"],
"description": "input that defines type of illumination correction to be performed"
},
"segmentation": {
"type": "string",
"pattern": "^((cellpose|mesmer)?,?)*(?<!,)$",
"description": "comma separated list of segmentation modules to run. options are ['mesmer','cellpose']"
},
"cellpose_model": {
"type": "string",
"description": "optional model file for cellpose segmentation"
}
}
},
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5 changes: 5 additions & 0 deletions subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,11 @@ def validateInputParameters() {
} else if(!params.input_sample && !params.input_cycle) {
error "You must specify either input_sample or input_cycle."
}

if (params.cellpose_model && !segmentation_list.contains('cellpose')) {
error "You can only provide a cellpose model if you have selected cellpose as one of your segmentation methods"
}

}

//
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145 changes: 136 additions & 9 deletions tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,9 @@ nextflow_workflow {
test("cycle: no illumination correction") {

when {
params {
segmentation = "mesmer"
}
workflow {
"""
input[0] = Channel.of(
Expand Down Expand Up @@ -37,7 +40,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/TEST1.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
).match()
},
{ assert workflow.success }
Expand All @@ -51,6 +54,7 @@ nextflow_workflow {
when {
params {
illumination = "basicpy"
segmentation = "mesmer"
}
workflow {
"""
Expand Down Expand Up @@ -80,7 +84,7 @@ nextflow_workflow {
assert snapshot (
ImageUtils.getImageMetadata("$outputDir/registration/ashlar/TEST1.ome.tif"),
ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff")
).match()
Expand All @@ -95,6 +99,7 @@ nextflow_workflow {
when {
params {
illumination = "manual"
segmentation = "mesmer"
}
workflow {
"""
Expand Down Expand Up @@ -124,7 +129,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/TEST1.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv")
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/TEST1_mask_TEST1.csv")
).match()
},
{ assert workflow.success }
Expand All @@ -135,6 +140,9 @@ nextflow_workflow {
test("cycle: multiple file ashlar input no correction") {

when {
params {
segmentation = "mesmer"
}
workflow {
"""
input[0] = Channel.of(
Expand Down Expand Up @@ -183,7 +191,7 @@ nextflow_workflow {
assert snapshot (
path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv")
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv")
).match()
},
{ assert workflow.success }
Expand All @@ -194,6 +202,76 @@ nextflow_workflow {
test("cycle: multiple file ashlar input with multiple samples no correction") {

when {
params {
segmentation = "mesmer"
}
workflow {
"""
input[0] = Channel.of(
[
[id:"cycif-tonsil", cycle_number:1, channel_count:4],
"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif",
[],
[],
],
[
[id:"cycif-tonsil", cycle_number:2, channel_count:4],
"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif",
[],
[],
],
[
[id:"cycif-tonsil2", cycle_number:1, channel_count:4],
"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif",
[],
[],
],
[
[id:"cycif-tonsil2", cycle_number:2, channel_count:4],
"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif",
[],
[],
],
)
input[1] = Channel.of(
[
[1,1,'DNA_6',[],[],[]],
[2,1,'ELANE',[],[],[]],
[3,1,'CD57',[],[],[]],
[4,1,'CD45',[],[],[]],
[5,1,'DNA_7',[],[],[]],
[6,1,'ELANE7',[],[],[]],
[7,1,'CD577',[],[],[]],
[8,1,'CD457',[],[],[]],
],
)
"""
}
}

then {
assertAll (
{
assert snapshot (
path("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
).match()
},
{ assert workflow.success }
)
}
},

test("cycle: multiple file ashlar input with multiple samples no correction, multiple segmentation") {

when {
params {
segmentation = "mesmer,cellpose"
}
workflow {
"""
input[0] = Channel.of(
Expand Down Expand Up @@ -246,8 +324,12 @@ nextflow_workflow {
path("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cycif-tonsil2_mask_cycif-tonsil2.csv"),
path("$outputDir/segmentation/cellpose/cycif-tonsil.ome_cp_masks.tif"),
path("$outputDir/segmentation/cellpose/cycif-tonsil2.ome_cp_masks.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil_cycif-tonsil.csv"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/cycif-tonsil2_cycif-tonsil2.csv"),
).match()
},
{ assert workflow.success }
Expand All @@ -260,6 +342,7 @@ nextflow_workflow {
when {
params {
illumination = "basicpy"
segmentation = "mesmer"
}
workflow {
"""
Expand Down Expand Up @@ -309,7 +392,7 @@ nextflow_workflow {
assert snapshot (
ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
Expand All @@ -328,6 +411,7 @@ nextflow_workflow {
when {
params {
illumination = "basicpy"
segmentation = "mesmer"
}
workflow {
"""
Expand Down Expand Up @@ -381,8 +465,8 @@ nextflow_workflow {
ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil2.ome.tif"),
ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil2_mask_cycif-tonsil2.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil_mask_cycif-tonsil.csv"),
CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/mesmer/cycif-tonsil2_mask_cycif-tonsil2.csv"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
Expand All @@ -396,5 +480,48 @@ nextflow_workflow {
}
},

test("cycle: no illumination correction, cellpose segmentation") {

when {
params {
segmentation = "cellpose"
}
workflow {
"""
input[0] = Channel.of(
[
[id:"TEST1", cycle_number:1, channel_count:4],
"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif",
[],
[],
],
)
input[1] = Channel.of(
[
[1,1,'DNA_6',[],[],[]],
[2,1,'ELANE',[],[],[]],
[3,1,'CD57',[],[],[]],
[4,1,'CD45',[],[],[]],
],
)
"""
}
}

then {
assertAll (
{
assert snapshot (
path("$outputDir/registration/ashlar/TEST1.ome.tif"),
path("$outputDir/segmentation/cellpose/TEST1.ome_cp_masks.tif"),
CsvUtils.roundAndHashCsv("$outputDir/quantification/mcquant/cellpose/TEST1_TEST1.csv"),
).match()
},
{ assert workflow.success }
)
}

},

]
}
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