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kelly-sovacoolkelly-sovacool
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feat: add all MOSuite capsules
1 parent a2445b0 commit a6c8d39

4 files changed

Lines changed: 309 additions & 9 deletions

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‎.codeocean/app-panel.json‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,9 @@
1919
"capsule_mosuite_filter_differential_expression_results_11",
2020
"capsule_mosuite_plot_expression_heatmap_12",
2121
"capsule_mosuite_plot_2_d_pca_13",
22-
"capsule_mosuite_plot_3_d_pca_14"
22+
"capsule_mosuite_plot_3_d_pca_14",
23+
"capsule_mosuite_plot_volcano_enhanced_15",
24+
"capsule_mosuite_plot_volcano_summary_16",
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"capsule_mosuite_plot_venn_diagram_17"
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]
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}

‎.codeocean/nextflow.json‎

Lines changed: 78 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -244,6 +244,84 @@
244244
"results": {
245245
"id": "a160b105-3084-46fc-8cc9-02886fd4bacb"
246246
}
247+
},
248+
{
249+
"name": "capsule_mosuite_plot_volcano_enhanced_15",
250+
"capsule": {
251+
"id": "4fbfaf69-b582-4533-8e00-f138caa869d1",
252+
"name": "MOSuite - Plot Volcano Enhanced",
253+
"slug": "7581039",
254+
"version": 1,
255+
"app_panel": true
256+
},
257+
"resources": {
258+
"cpus": 1,
259+
"memory": 8
260+
},
261+
"inputs": [
262+
{
263+
"id": "FrEEXOAv8b9ynjCQ",
264+
"source_id": "capsule_mosuite_filter_differential_expression_results_11",
265+
"type": "capsule",
266+
"name": "MOSuite - filter differential expression results",
267+
"collect": true
268+
}
269+
],
270+
"results": {
271+
"id": "4fbfaf69-b582-4533-8e00-f138caa869d1"
272+
}
273+
},
274+
{
275+
"name": "capsule_mosuite_plot_volcano_summary_16",
276+
"capsule": {
277+
"id": "f47f9943-0628-44d3-ae81-b2ed11d73817",
278+
"name": "MOSuite - Plot Volcano Summary",
279+
"slug": "6849617",
280+
"version": 2,
281+
"app_panel": true
282+
},
283+
"resources": {
284+
"cpus": 1,
285+
"memory": 8
286+
},
287+
"inputs": [
288+
{
289+
"id": "Lw7lIWW4xBeK3fLq",
290+
"source_id": "capsule_mosuite_filter_differential_expression_results_11",
291+
"type": "capsule",
292+
"name": "MOSuite - filter differential expression results",
293+
"collect": true
294+
}
295+
],
296+
"results": {
297+
"id": "f47f9943-0628-44d3-ae81-b2ed11d73817"
298+
}
299+
},
300+
{
301+
"name": "capsule_mosuite_plot_venn_diagram_17",
302+
"capsule": {
303+
"id": "b18a7c9b-d66b-4921-9df8-0cfa88a4a35a",
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"name": "MOSuite - Plot Venn Diagram",
305+
"slug": "5013652",
306+
"version": 1,
307+
"app_panel": true
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},
309+
"resources": {
310+
"cpus": 1,
311+
"memory": 8
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},
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"inputs": [
314+
{
315+
"id": "qDPGXdGH6MI1JgSO",
316+
"source_id": "capsule_mosuite_filter_differential_expression_results_11",
317+
"type": "capsule",
318+
"name": "MOSuite - filter differential expression results",
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"collect": true
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}
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],
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"results": {
323+
"id": "b18a7c9b-d66b-4921-9df8-0cfa88a4a35a"
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}
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}
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]
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}

‎.codeocean/pipeline-layout.json‎

Lines changed: 76 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -83,14 +83,47 @@
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"id": "xy-edge__capsule_mosuite_plot_expression_heatmap_12-results",
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"source": "capsule_mosuite_plot_expression_heatmap_12",
8585
"target": "results"
86+
},
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{
88+
"id": "xy-edge__capsule_mosuite_filter_differential_expression_results_11-capsule_mosuite_plot_volcano_enhanced_15",
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"selected": false,
90+
"source": "capsule_mosuite_filter_differential_expression_results_11",
91+
"target": "capsule_mosuite_plot_volcano_enhanced_15"
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},
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{
94+
"id": "xy-edge__capsule_mosuite_filter_differential_expression_results_11-capsule_mosuite_plot_volcano_summary_16",
95+
"selected": false,
96+
"source": "capsule_mosuite_filter_differential_expression_results_11",
97+
"target": "capsule_mosuite_plot_volcano_summary_16"
98+
},
99+
{
100+
"id": "xy-edge__capsule_mosuite_filter_differential_expression_results_11-capsule_mosuite_plot_venn_diagram_17",
101+
"selected": false,
102+
"source": "capsule_mosuite_filter_differential_expression_results_11",
103+
"target": "capsule_mosuite_plot_venn_diagram_17"
104+
},
105+
{
106+
"id": "xy-edge__capsule_mosuite_plot_volcano_enhanced_15-results",
107+
"source": "capsule_mosuite_plot_volcano_enhanced_15",
108+
"target": "results"
109+
},
110+
{
111+
"id": "xy-edge__capsule_mosuite_plot_volcano_summary_16-results",
112+
"source": "capsule_mosuite_plot_volcano_summary_16",
113+
"target": "results"
114+
},
115+
{
116+
"id": "xy-edge__capsule_mosuite_plot_venn_diagram_17-results",
117+
"source": "capsule_mosuite_plot_venn_diagram_17",
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"target": "results"
86119
}
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],
88121
"nodes": [
89122
{
90123
"id": "results",
91124
"position": {
92-
"x": 1587.658058657255,
93-
"y": 1600.3872578624141
125+
"x": 1756.4571308404495,
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"y": 1986.2137085668587
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},
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"selected": false,
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"type": "results"
@@ -173,7 +206,7 @@
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"x": 1421.2854093431497,
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"y": 700.0248604406177
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},
176-
"selected": true,
209+
"selected": false,
177210
"type": "capsule"
178211
},
179212
{
@@ -223,12 +256,48 @@
223256
},
224257
"selected": false,
225258
"type": "capsule"
259+
},
260+
{
261+
"data": {
262+
"capsule_id": "4fbfaf69-b582-4533-8e00-f138caa869d1"
263+
},
264+
"id": "capsule_mosuite_plot_volcano_enhanced_15",
265+
"position": {
266+
"x": 1751.8349639754883,
267+
"y": 1413.074496418595
268+
},
269+
"selected": false,
270+
"type": "capsule"
271+
},
272+
{
273+
"data": {
274+
"capsule_id": "f47f9943-0628-44d3-ae81-b2ed11d73817"
275+
},
276+
"id": "capsule_mosuite_plot_volcano_summary_16",
277+
"position": {
278+
"x": 2003.6938970742233,
279+
"y": 1445.2267006439652
280+
},
281+
"selected": false,
282+
"type": "capsule"
283+
},
284+
{
285+
"data": {
286+
"capsule_id": "b18a7c9b-d66b-4921-9df8-0cfa88a4a35a"
287+
},
288+
"id": "capsule_mosuite_plot_venn_diagram_17",
289+
"position": {
290+
"x": 2252.8734798208434,
291+
"y": 1461.3028027566504
292+
},
293+
"selected": true,
294+
"type": "capsule"
226295
}
227296
],
228-
"timestamp": 1770239945557,
297+
"timestamp": 1770317162918,
229298
"viewport": {
230-
"x": -375.194647645313,
231-
"y": -165.89459366008077,
232-
"zoom": 0.5071432609245071
299+
"x": -298.82825452190866,
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"y": -50.89444668129266,
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"zoom": 0.37322480026209653
233302
}
234303
}

‎pipeline/main.nf‎

Lines changed: 151 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
#!/usr/bin/env nextflow
2-
// hash:sha256:8af9c2ae045034467f259ee9b540d9e5c3ecb5dfbe1d919635f7c6f187c7e507
2+
// hash:sha256:0585bc1421e1b8a641cac81981069265b8bf822b02a9763632ff71dd01c114b0
33

44
// capsule - MOSuite - create multiOmicDataSet
55
process capsule_mosuite_create_multiomicdataset_4 {
@@ -297,6 +297,9 @@ process capsule_mosuite_filter_differential_expression_results_11 {
297297

298298
output:
299299
path 'capsule/results/*'
300+
path 'capsule/results/*', emit: to_capsule_mosuite_plot_volcano_enhanced_15_10
301+
path 'capsule/results/*', emit: to_capsule_mosuite_plot_volcano_summary_16_11
302+
path 'capsule/results/*', emit: to_capsule_mosuite_plot_venn_diagram_17_12
300303

301304
script:
302305
"""
@@ -474,6 +477,150 @@ process capsule_mosuite_plot_expression_heatmap_12 {
474477
"""
475478
}
476479

480+
// capsule - MOSuite - Plot Venn Diagram
481+
process capsule_mosuite_plot_venn_diagram_17 {
482+
tag 'capsule-5013652'
483+
container "$REGISTRY_HOST/published/b18a7c9b-d66b-4921-9df8-0cfa88a4a35a:v1"
484+
485+
cpus 1
486+
memory '7.5 GB'
487+
488+
publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
489+
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input:
491+
path 'capsule/data/'
492+
493+
output:
494+
path 'capsule/results/*'
495+
496+
script:
497+
"""
498+
#!/usr/bin/env bash
499+
set -e
500+
501+
export CO_CAPSULE_ID=b18a7c9b-d66b-4921-9df8-0cfa88a4a35a
502+
export CO_CPUS=1
503+
export CO_MEMORY=8053063680
504+
505+
mkdir -p capsule
506+
mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
507+
mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
508+
mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
509+
510+
echo "[${task.tag}] cloning git repo..."
511+
if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
512+
git clone --filter=tree:0 --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5013652.git" capsule-repo
513+
else
514+
git clone --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5013652.git" capsule-repo
515+
fi
516+
mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
517+
rm -rf capsule-repo
518+
519+
echo "[${task.tag}] running capsule..."
520+
cd capsule/code
521+
chmod +x run
522+
./run ${params.capsule_mosuite_plot_venn_diagram_17_args}
523+
524+
echo "[${task.tag}] completed!"
525+
"""
526+
}
527+
528+
// capsule - MOSuite - Plot Volcano Enhanced
529+
process capsule_mosuite_plot_volcano_enhanced_15 {
530+
tag 'capsule-7581039'
531+
container "$REGISTRY_HOST/published/4fbfaf69-b582-4533-8e00-f138caa869d1:v1"
532+
533+
cpus 1
534+
memory '7.5 GB'
535+
536+
publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
537+
538+
input:
539+
path 'capsule/data/'
540+
541+
output:
542+
path 'capsule/results/*'
543+
544+
script:
545+
"""
546+
#!/usr/bin/env bash
547+
set -e
548+
549+
export CO_CAPSULE_ID=4fbfaf69-b582-4533-8e00-f138caa869d1
550+
export CO_CPUS=1
551+
export CO_MEMORY=8053063680
552+
553+
mkdir -p capsule
554+
mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
555+
mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
556+
mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
557+
558+
echo "[${task.tag}] cloning git repo..."
559+
if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
560+
git clone --filter=tree:0 --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-7581039.git" capsule-repo
561+
else
562+
git clone --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-7581039.git" capsule-repo
563+
fi
564+
mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
565+
rm -rf capsule-repo
566+
567+
echo "[${task.tag}] running capsule..."
568+
cd capsule/code
569+
chmod +x run
570+
./run ${params.capsule_mosuite_plot_volcano_enhanced_15_args}
571+
572+
echo "[${task.tag}] completed!"
573+
"""
574+
}
575+
576+
// capsule - MOSuite - Plot Volcano Summary
577+
process capsule_mosuite_plot_volcano_summary_16 {
578+
tag 'capsule-6849617'
579+
container "$REGISTRY_HOST/published/f47f9943-0628-44d3-ae81-b2ed11d73817:v2"
580+
581+
cpus 1
582+
memory '7.5 GB'
583+
584+
publishDir "$RESULTS_PATH", saveAs: { filename -> new File(filename).getName() }
585+
586+
input:
587+
path 'capsule/data/'
588+
589+
output:
590+
path 'capsule/results/*'
591+
592+
script:
593+
"""
594+
#!/usr/bin/env bash
595+
set -e
596+
597+
export CO_CAPSULE_ID=f47f9943-0628-44d3-ae81-b2ed11d73817
598+
export CO_CPUS=1
599+
export CO_MEMORY=8053063680
600+
601+
mkdir -p capsule
602+
mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
603+
mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
604+
mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
605+
606+
echo "[${task.tag}] cloning git repo..."
607+
if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
608+
git clone --filter=tree:0 --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6849617.git" capsule-repo
609+
else
610+
git clone --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6849617.git" capsule-repo
611+
fi
612+
mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
613+
rm -rf capsule-repo
614+
615+
echo "[${task.tag}] running capsule..."
616+
cd capsule/code
617+
chmod +x run
618+
./run ${params.capsule_mosuite_plot_volcano_summary_16_args}
619+
620+
echo "[${task.tag}] completed!"
621+
"""
622+
}
623+
477624
workflow {
478625
// run processes
479626
capsule_mosuite_create_multiomicdataset_4()
@@ -486,4 +633,7 @@ workflow {
486633
capsule_mosuite_plot_2_d_pca_13(capsule_mosuite_normalize_counts_7.out.to_capsule_mosuite_plot_2_d_pca_13_8.collect())
487634
capsule_mosuite_plot_3_d_pca_14(capsule_mosuite_normalize_counts_7.out.to_capsule_mosuite_plot_3_d_pca_14_9.collect())
488635
capsule_mosuite_plot_expression_heatmap_12(capsule_mosuite_normalize_counts_7.out.to_capsule_mosuite_plot_expression_heatmap_12_7.collect())
636+
capsule_mosuite_plot_venn_diagram_17(capsule_mosuite_filter_differential_expression_results_11.out.to_capsule_mosuite_plot_venn_diagram_17_12.collect())
637+
capsule_mosuite_plot_volcano_enhanced_15(capsule_mosuite_filter_differential_expression_results_11.out.to_capsule_mosuite_plot_volcano_enhanced_15_10.collect())
638+
capsule_mosuite_plot_volcano_summary_16(capsule_mosuite_filter_differential_expression_results_11.out.to_capsule_mosuite_plot_volcano_summary_16_11.collect())
489639
}

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