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Merged
khersameesh24 merged 2 commits into from
Oct 25, 2025
Merged

Codespace scaling giggle 4vrjwqp5rv4375jr #10

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99401e7
Pending changes exported from your codespace
khersameesh24 Oct 23, 2025
547d9f1
added support for baysor preview html in multiqc report
khersameesh24 Oct 25, 2025
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2 changes: 1 addition & 1 deletion assets/samplesheet.csv
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@@ -1,2 +1,2 @@
sample,bundle,image
Xenium_Prime_Mouse_Ileum_tiny_outs,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.tar.gz,
test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz
18 changes: 18 additions & 0 deletions conf/modules.config
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Expand Up @@ -27,6 +27,24 @@ process {
]
}

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

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

withName: XENIUMRANGER_RESEGMENT {
publishDir = [
path: "${params.outdir}/xeniumranger/resegment",
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4 changes: 4 additions & 0 deletions conf/test.config
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Expand Up @@ -18,6 +18,10 @@ process {
time: '2.h',
]

withName: UNTAR {
ext.prefix = "test_run"
}

}

params {
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31 changes: 31 additions & 0 deletions conf/test_coordinate_mode.config
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@@ -0,0 +1,31 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {

resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '2.h',
]

}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'coordinate'
}
31 changes: 31 additions & 0 deletions conf/test_image_mode.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {

resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '2.h',
]

}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'image'
}
31 changes: 31 additions & 0 deletions conf/test_preview_mode.config
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@@ -0,0 +1,31 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {

resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '2.h',
]

}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'preview'
}
31 changes: 31 additions & 0 deletions conf/test_segfree_mode.config
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@@ -0,0 +1,31 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.

Use as follows:
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {

resourceLimits = [
cpus: 4,
memory: '15.GB',
time: '2.h',
]

}

params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'segfree'
}
54 changes: 40 additions & 14 deletions modules.json
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Expand Up @@ -8,59 +8,79 @@
"cellpose": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/cellpose/cellpose.diff"
},
"multiqc": {
"branch": "master",
"git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"opt/flip": {
"branch": "master",
"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/opt/flip/opt-flip.diff"
},
"opt/stat": {
"branch": "master",
"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/opt/stat/opt-stat.diff"
},
"opt/track": {
"branch": "master",
"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/opt/track/opt-track.diff"
},
"untar": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/untar/untar.diff"
},
"unzip": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"xeniumranger/import-segmentation": {
"branch": "master",
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff"
},
"xeniumranger/relabel": {
"branch": "master",
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/xeniumranger/relabel/xeniumranger-relabel.diff"
},
"xeniumranger/resegment": {
"branch": "master",
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
"installed_by": ["modules"],
"installed_by": [
"modules"
],
"patch": "modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff"
}
}
Expand All @@ -70,20 +90,26 @@
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
}
}
}
}
}
}
}
5 changes: 2 additions & 3 deletions modules/local/baysor/preview/main.nf
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Expand Up @@ -29,10 +29,9 @@ process BAYSOR_PREVIEW {
baysor preview \\
${transcripts} \\
--config ${config} \\
--output ${prefix}/preview.html
${args}

mv preview.html ${prefix}/preview.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
baysor: 0.7.1
Expand All @@ -49,7 +48,7 @@ process BAYSOR_PREVIEW {

"""
mkdir -p ${prefix}
touch "${prefix}/preview.html"
touch ${prefix}/preview.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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43 changes: 43 additions & 0 deletions modules/local/utility/clean_html/main.nf
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process CLEAN_PREVIEW_HTML {
tag "${meta.id}"
label 'process_low'

container "community.wave.seqera.io/library/beautifulsoup4_procs:3f09125465990b35"

input:
tuple val(meta), path(preview_html)

output:
tuple val(meta), path("${prefix}/preview_mqc.html"), emit: mqc_html
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("CLEAN_HTML module does not support Conda. Please use Docker / Singularity / Podman instead.")
}

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

template('clean_html.py')

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

"""
mkdir -p ${prefix}
touch ${prefix}/preview_mqc.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
CLEAN_HTML: "1.0.0"
END_VERSIONS
"""
}
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