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Merged
khersameesh24 merged 3 commits into from
Oct 20, 2025
Merged

Testing changes and code formatting #103

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169a11f
testing changes and code formatting
khersameesh24 Oct 10, 2025
b05ab94
pre-commit fix
khersameesh24 Oct 10, 2025
89b52e8
tif resizing based on transcript coordinates
khersameesh24 Oct 14, 2025
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15 changes: 0 additions & 15 deletions assets/multiqc_config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,18 +15,3 @@ export_plots: true
disable_version_detection: true

log_filesize_limit: 5000000000 # 5GB

sp:
xenium/cell_feature_matrix:
fn: "*/cell_feature_matrix.h5"
xenium/cells:
fn: "*/cells.parquet"
xenium/experiment:
fn: "*/experiment.xenium"
num_lines: 50
xenium/metrics:
contents: num_cells_detected
fn: "*/metrics_summary.csv"
num_lines: 5
xenium/transcripts:
fn: "*/transcripts.parquet"
40 changes: 20 additions & 20 deletions conf/base.config
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Expand Up @@ -11,9 +11,9 @@
process {

// nf-core: Check the defaults for all processes
cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
cpus = { 1 * task.attempt }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }

errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
maxRetries = 1
Expand All @@ -26,36 +26,36 @@ process {
// adding in your local modules too.
// nf-core: Customise requirements for specific processes.
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
withLabel:process_single {
cpus = { 1 }
withLabel: process_single {
cpus = { 1 }
memory = { 6.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_low {
cpus = { 2 * task.attempt }
withLabel: process_low {
cpus = { 2 * task.attempt }
memory = { 12.GB * task.attempt }
time = { 4.h * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_medium {
cpus = { 6 * task.attempt }
withLabel: process_medium {
cpus = { 6 * task.attempt }
memory = { 36.GB * task.attempt }
time = { 8.h * task.attempt }
time = { 8.h * task.attempt }
}
withLabel:process_high {
cpus = { 12 * task.attempt }
withLabel: process_high {
cpus = { 12 * task.attempt }
memory = { 72.GB * task.attempt }
time = { 16.h * task.attempt }
time = { 16.h * task.attempt }
}
withLabel:process_long {
time = { 20.h * task.attempt }
withLabel: process_long {
time = { 20.h * task.attempt }
}
withLabel:process_high_memory {
withLabel: process_high_memory {
memory = { 200.GB * task.attempt }
}
withLabel:error_ignore {
withLabel: error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
withLabel: error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
Expand Down
24 changes: 11 additions & 13 deletions conf/modules.config
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Expand Up @@ -15,38 +15,36 @@ process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]

withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
withName: MULTIQC {
ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}

withName: XENIUMRANGER_RESEGMENT {
publishDir = [
path: "${params.outdir}/xeniumranger/resegment",
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
]
ext.prefix = {"${meta.id}"}
}

withName: XENIUMRANGER_IMPORT_SEGMENTATION {
publishDir = [
path: "${params.outdir}/xeniumranger/import_segementation",
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
]
ext.prefix = {"${meta.id}"}
}

withName: FICTURE_PREPROCESS {
publishDir = [
path: "${params.outdir}/ficture/preprocess",
mode: params.publish_dir_mode
mode: params.publish_dir_mode,
]
}

Expand Down Expand Up @@ -90,7 +88,7 @@ process {
path: { "${params.outdir}/segger/train" },
mode: params.publish_dir_mode,
]
ext.args = { "--init_emb 8 --hidden_channels 32 --num_tx_tokens 500 --out_channels 8 --heads 2 --num_mid_layers 2 --strategy auto --precision 16-mixed" }
ext.args = { "--init_emb 8 --hidden_channels 32 --num_tx_tokens 500 --out_channels 8 --heads 2 --num_mid_layers 2 --strategy auto --precision 16-mixed" }
}

withName: SEGGER_PREDICT {
Expand Down Expand Up @@ -133,7 +131,7 @@ process {
path: { "${params.outdir}/cellpose" },
mode: params.publish_dir_mode,
]
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
}

// with new version of cellpose you can do --output_name cell_masks
Expand All @@ -142,7 +140,7 @@ process {
path: { "${params.outdir}/cellpose_cells" },
mode: params.publish_dir_mode,
]
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
}

// with new version of cellpose you can do --output_name nucleus_masks
Expand All @@ -151,7 +149,7 @@ process {
path: { "${params.outdir}/cellpose_nuclei" },
mode: params.publish_dir_mode,
]
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
ext.args = { "--diameter 9 --channel_axis 0 --save_flows" }
}

withName: OPT_FLIP {
Expand Down
2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -17,5 +17,5 @@ params {
// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'image'
mode = 'coordinate'
}
12 changes: 6 additions & 6 deletions modules/local/baysor/create_dataset/main.nf
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@@ -1,34 +1,34 @@
process BAYSOR_CREATE_DATASET {
tag "$meta.id"
tag "${meta.id}"
label 'process_medium'

container "khersameesh24/baysor:0.7.1"

input:
tuple val(meta), path(transcripts)
val(sample_fraction)
val sample_fraction

output:
tuple val(meta), path("${prefix}/sampled_transcripts.csv"), emit: sampled_transcripts
path("versions.yml") , emit: versions
path ("versions.yml"), emit: versions

when:
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_CREATE_DATASET module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_CREATE_DATASET module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"

template 'create_dataset.py'
template('create_dataset.py')

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_CREATE_DATASET module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_CREATE_DATASET module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"
Expand Down
23 changes: 11 additions & 12 deletions modules/local/baysor/preprocess/main.nf
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@@ -1,39 +1,38 @@
process BAYSOR_PREPROCESS_TRANSCRIPTS {
tag "$meta.id"
tag "${meta.id}"
label 'process_low'

container "ghcr.io/scverse/spatialdata:spatialdata0.3.0_spatialdata-io0.1.7_spatialdata-plot0.2.9"

input:
tuple val(meta), path(transcripts)
val(min_qv)
val(max_x)
val(min_x)
val(max_y)
val(min_y)
val min_qv
val max_x
val min_x
val max_y
val min_y

output:
tuple val(meta),
path("${prefix}/filtered_transcripts.parquet"), emit: transcripts_parquet
path("versions.yml") , emit: versions
tuple val(meta), path("${prefix}/filtered_transcripts.parquet"), emit: transcripts_parquet
path ("versions.yml"), emit: versions

when:
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_PREPROCESS_TRANSCRIPTS module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_PREPROCESS_TRANSCRIPTS module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"

template 'preprocess_transcripts.py'
template('preprocess_transcripts.py')

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_PREPROCESS_TRANSCRIPTS module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_PREPROCESS_TRANSCRIPTS module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"
Expand Down
10 changes: 5 additions & 5 deletions modules/local/baysor/preview/main.nf
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@@ -1,24 +1,24 @@
process BAYSOR_PREVIEW {
tag "$meta.id"
tag "${meta.id}"
label 'process_high'

container "khersameesh24/baysor:0.7.1"

input:
tuple val(meta), path(transcripts)
path(config)
path config

output:
tuple val(meta), path("${prefix}/preview.html"), emit: preview_html
path("versions.yml") , emit: versions
path ("versions.yml"), emit: versions

when:
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

def args = task.ext.args ?: ''
Expand All @@ -43,7 +43,7 @@ process BAYSOR_PREVIEW {
stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"
Expand Down
20 changes: 7 additions & 13 deletions modules/local/baysor/run/main.nf
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@@ -1,34 +1,28 @@
process BAYSOR_RUN {
tag "$meta.id"
tag "${meta.id}"
label 'process_high'

container "khersameesh24/baysor:0.7.1"

input:
tuple val(meta),
path(transcripts),
path(prior_segmentation),
path(config),
val(scale)
tuple val(meta), path(transcripts), path(prior_segmentation), path(config), val(scale)

output:
tuple val(meta),
path("${prefix}/segmentation.csv"),
path("${prefix}/segmentation_polygons_2d.json"), emit: segmentation
path("versions.yml") , emit: versions
tuple val(meta), path("${prefix}/segmentation.csv"), path("${prefix}/segmentation_polygons_2d.json"), emit: segmentation
path ("versions.yml"), emit: versions

when:
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

def args = task.ext.args ?: ''
def prior_seg = "${prior_segmentation}" ? "${prior_segmentation}" : ""
def scaling_factor = scale ? "--scale=${scale}": ""
def scaling_factor = scale ? "--scale=${scale}" : ""
prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand All @@ -53,7 +47,7 @@ process BAYSOR_RUN {
stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"
Expand Down
10 changes: 5 additions & 5 deletions modules/local/baysor/segfree/main.nf
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@@ -1,24 +1,24 @@
process BAYSOR_SEGFREE {
tag "$meta.id"
tag "${meta.id}"
label 'process_high'

container "khersameesh24/baysor:0.7.1"

input:
tuple val(meta), path(transcripts)
path(config)
path config

output:
tuple val(meta), path("${prefix}/ncvs.loom"), emit: ncvs
path("versions.yml") , emit: versions
path ("versions.yml"), emit: versions

when:
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_SEGFREE module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_SEGFREE module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

def args = task.ext.args ?: ''
Expand All @@ -42,7 +42,7 @@ process BAYSOR_SEGFREE {
stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BAYSOR_SEGFREE module does not support Conda. Please use Docker / Singularity / Podman instead."
error("BAYSOR_SEGFREE module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

prefix = task.ext.prefix ?: "${meta.id}"
Expand Down
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