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khersameesh24khersameesh24
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Merge pull request #10 from khersameesh24/codespace-scaling-giggle-4vrjwqp5rv4375jr
Codespace scaling giggle 4vrjwqp5rv4375jr
2 parents bc2cc6d + 547d9f1 commit 86b47fa

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-243
lines changed

32 files changed

+903
-243
lines changed

‎assets/samplesheet.csv‎

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@@ -1,2 +1,2 @@
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sample,bundle,image
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Xenium_Prime_Mouse_Ileum_tiny_outs,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.tar.gz,
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test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz

‎conf/modules.config‎

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@@ -27,6 +27,24 @@ process {
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]
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}
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withName: MULTIQC_PRE_XR_RUN {
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ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
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publishDir = [
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path: { "${params.outdir}/multiqc/raw_bundle" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
36+
]
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}
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withName: MULTIQC_POST_XR_RUN {
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ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
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publishDir = [
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path: { "${params.outdir}/multiqc/redefined_bundle" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
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]
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}
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withName: XENIUMRANGER_RESEGMENT {
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publishDir = [
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path: "${params.outdir}/xeniumranger/resegment",

‎conf/test.config‎

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@@ -18,6 +18,10 @@ process {
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time: '2.h',
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]
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withName: UNTAR {
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ext.prefix = "test_run"
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}
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}
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params {

‎conf/test_coordinate_mode.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
6+
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Use as follows:
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nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
9+
10+
----------------------------------------------------------------------------------------
11+
*/
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process {
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resourceLimits = [
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cpus: 4,
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memory: '15.GB',
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time: '2.h',
19+
]
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}
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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input = "${projectDir}/assets/samplesheet.csv"
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outdir = 'results'
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mode = 'coordinate'
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}

‎conf/test_image_mode.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
4+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5+
Defines input files and everything required to run a fast and simple pipeline test.
6+
7+
Use as follows:
8+
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
9+
10+
----------------------------------------------------------------------------------------
11+
*/
12+
13+
process {
14+
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resourceLimits = [
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cpus: 4,
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memory: '15.GB',
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time: '2.h',
19+
]
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}
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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// Input data
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input = "${projectDir}/assets/samplesheet.csv"
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outdir = 'results'
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mode = 'image'
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}

‎conf/test_preview_mode.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5+
Defines input files and everything required to run a fast and simple pipeline test.
6+
7+
Use as follows:
8+
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
9+
10+
----------------------------------------------------------------------------------------
11+
*/
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process {
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resourceLimits = [
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cpus: 4,
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memory: '15.GB',
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time: '2.h',
19+
]
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}
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params {
24+
config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
26+
27+
// Input data
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input = "${projectDir}/assets/samplesheet.csv"
29+
outdir = 'results'
30+
mode = 'preview'
31+
}

‎conf/test_segfree_mode.config‎

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/*
2+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
4+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5+
Defines input files and everything required to run a fast and simple pipeline test.
6+
7+
Use as follows:
8+
nextflow run nf-core/spatialxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
9+
10+
----------------------------------------------------------------------------------------
11+
*/
12+
13+
process {
14+
15+
resourceLimits = [
16+
cpus: 4,
17+
memory: '15.GB',
18+
time: '2.h',
19+
]
20+
21+
}
22+
23+
params {
24+
config_profile_name = 'Test profile'
25+
config_profile_description = 'Minimal test dataset to check pipeline function'
26+
27+
// Input data
28+
input = "${projectDir}/assets/samplesheet.csv"
29+
outdir = 'results'
30+
mode = 'segfree'
31+
}

‎modules.json‎

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@@ -8,59 +8,79 @@
88
"cellpose": {
99
"branch": "master",
1010
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
11-
"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/cellpose/cellpose.diff"
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
17-
"installed_by": ["modules"]
19+
"installed_by": [
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"modules"
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]
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},
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"opt/flip": {
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"branch": "master",
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"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
22-
"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/opt/flip/opt-flip.diff"
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},
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"opt/stat": {
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"branch": "master",
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"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
28-
"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/opt/stat/opt-stat.diff"
3038
},
3139
"opt/track": {
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"branch": "master",
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"git_sha": "66d5baa4e9b6ac3ab95e84f88709b8e3ebf4b62b",
34-
"installed_by": ["modules"],
42+
"installed_by": [
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"modules"
44+
],
3545
"patch": "modules/nf-core/opt/track/opt-track.diff"
3646
},
3747
"untar": {
3848
"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
40-
"installed_by": ["modules"],
50+
"installed_by": [
51+
"modules"
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],
4153
"patch": "modules/nf-core/untar/untar.diff"
4254
},
4355
"unzip": {
4456
"branch": "master",
4557
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
46-
"installed_by": ["modules"]
58+
"installed_by": [
59+
"modules"
60+
]
4761
},
4862
"xeniumranger/import-segmentation": {
4963
"branch": "master",
5064
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
51-
"installed_by": ["modules"],
65+
"installed_by": [
66+
"modules"
67+
],
5268
"patch": "modules/nf-core/xeniumranger/import-segmentation/xeniumranger-import-segmentation.diff"
5369
},
5470
"xeniumranger/relabel": {
5571
"branch": "master",
5672
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
57-
"installed_by": ["modules"],
73+
"installed_by": [
74+
"modules"
75+
],
5876
"patch": "modules/nf-core/xeniumranger/relabel/xeniumranger-relabel.diff"
5977
},
6078
"xeniumranger/resegment": {
6179
"branch": "master",
6280
"git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a",
63-
"installed_by": ["modules"],
81+
"installed_by": [
82+
"modules"
83+
],
6484
"patch": "modules/nf-core/xeniumranger/resegment/xeniumranger-resegment.diff"
6585
}
6686
}
@@ -70,20 +90,26 @@
7090
"utils_nextflow_pipeline": {
7191
"branch": "master",
7292
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
73-
"installed_by": ["subworkflows"]
93+
"installed_by": [
94+
"subworkflows"
95+
]
7496
},
7597
"utils_nfcore_pipeline": {
7698
"branch": "master",
7799
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
78-
"installed_by": ["subworkflows"]
100+
"installed_by": [
101+
"subworkflows"
102+
]
79103
},
80104
"utils_nfschema_plugin": {
81105
"branch": "master",
82106
"git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
83-
"installed_by": ["subworkflows"]
107+
"installed_by": [
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"subworkflows"
109+
]
84110
}
85111
}
86112
}
87113
}
88114
}
89-
}
115+
}

‎modules/local/baysor/preview/main.nf‎

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@@ -29,10 +29,9 @@ process BAYSOR_PREVIEW {
2929
baysor preview \\
3030
${transcripts} \\
3131
--config ${config} \\
32+
--output ${prefix}/preview.html
3233
${args}
3334
34-
mv preview.html ${prefix}/preview.html
35-
3635
cat <<-END_VERSIONS > versions.yml
3736
"${task.process}":
3837
baysor: 0.7.1
@@ -49,7 +48,7 @@ process BAYSOR_PREVIEW {
4948

5049
"""
5150
mkdir -p ${prefix}
52-
touch "${prefix}/preview.html"
51+
touch ${prefix}/preview.html
5352
5453
cat <<-END_VERSIONS > versions.yml
5554
"${task.process}":

‎modules/local/utility/clean_html/main.nf‎

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1+
process CLEAN_PREVIEW_HTML {
2+
tag "${meta.id}"
3+
label 'process_low'
4+
5+
container "community.wave.seqera.io/library/beautifulsoup4_procs:3f09125465990b35"
6+
7+
input:
8+
tuple val(meta), path(preview_html)
9+
10+
output:
11+
tuple val(meta), path("${prefix}/preview_mqc.html"), emit: mqc_html
12+
path ("versions.yml"), emit: versions
13+
14+
when:
15+
task.ext.when == null || task.ext.when
16+
17+
script:
18+
// Exit if running this module with -profile conda / -profile mamba
19+
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
20+
error("CLEAN_HTML module does not support Conda. Please use Docker / Singularity / Podman instead.")
21+
}
22+
23+
prefix = task.ext.prefix ?: "${meta.id}"
24+
25+
template('clean_html.py')
26+
27+
stub:
28+
// Exit if running this module with -profile conda / -profile mamba
29+
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
30+
error("CLEAN_HTML module does not support Conda. Please use Docker / Singularity / Podman instead.")
31+
}
32+
prefix = task.ext.prefix ?: "${meta.id}"
33+
34+
"""
35+
mkdir -p ${prefix}
36+
touch ${prefix}/preview_mqc.html
37+
38+
cat <<-END_VERSIONS > versions.yml
39+
"${task.process}":
40+
CLEAN_HTML: "1.0.0"
41+
END_VERSIONS
42+
"""
43+
}

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