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kelly-sovacoolkelly-sovacool
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Edited app-panel.json, nextflow.json, pipeline-layout.json, main.nf
1 parent 39a0053 commit a2445b0

4 files changed

Lines changed: 564 additions & 69 deletions

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‎.codeocean/app-panel.json‎

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@@ -1,10 +1,24 @@
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{
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"version": 1,
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"general": {
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"title": "MOSuite-pipeline"
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},
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"datasets": [
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{
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"id": "bd9a7518-66cb-4d50-9992-df3271aeb807",
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"name": "raw counts \u0026 samplesheet"
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}
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],
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"processes": [
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"capsule_mosuite_create_multiomicdataset_4",
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"capsule_mosuite_clean_raw_counts_5",
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"capsule_mosuite_filter_low_counts_6",
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"capsule_mosuite_normalize_counts_7",
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"capsule_mosuite_batch_correct_counts_8"
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"capsule_mosuite_clean_raw_counts_8",
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"capsule_mosuite_batch_correct_counts_9",
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"capsule_mosuite_differential_expression_analysis_10",
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"capsule_mosuite_filter_differential_expression_results_11",
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"capsule_mosuite_plot_expression_heatmap_12",
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"capsule_mosuite_plot_2_d_pca_13",
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"capsule_mosuite_plot_3_d_pca_14"
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]
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}

‎.codeocean/nextflow.json‎

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@@ -26,7 +26,53 @@
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]
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},
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{
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"name": "capsule_mosuite_clean_raw_counts_5",
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"name": "capsule_mosuite_filter_low_counts_6",
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"capsule": {
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"id": "0296f612-3498-4ed0-ac13-50620e45d67d",
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"name": "MOSuite - filter low counts",
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"slug": "4565215",
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"version": 1,
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"app_panel": true
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},
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"resources": {
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"cpus": 1,
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"memory": 8
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},
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"inputs": [
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{
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"id": "VFpVsmOmjj7FoaFm",
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"source_id": "capsule_mosuite_clean_raw_counts_8",
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"type": "capsule",
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"name": "MOSuite - clean raw counts",
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"collect": true
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}
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]
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},
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{
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"name": "capsule_mosuite_normalize_counts_7",
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"capsule": {
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"id": "75561d95-aa78-4140-b64d-ddae5b64fc39",
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"name": "MOSuite - normalize counts",
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"slug": "9169525",
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"version": 1,
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"app_panel": true
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},
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"resources": {
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"cpus": 1,
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"memory": 8
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},
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"inputs": [
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{
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"id": "QU4dCV5IbfyyUbob",
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"source_id": "capsule_mosuite_filter_low_counts_6",
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"type": "capsule",
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"name": "MOSuite - filter low counts",
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"collect": true
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}
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]
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},
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{
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"name": "capsule_mosuite_clean_raw_counts_8",
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"capsule": {
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"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b",
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"name": "MOSuite - clean raw counts",
@@ -40,20 +86,20 @@
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},
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"inputs": [
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{
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"id": "MpqDzOmjzI6k7acV",
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"id": "T696ioaNDR5F8bQy",
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"source_id": "capsule_mosuite_create_multiomicdataset_4",
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"type": "capsule",
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"name": "MOSuite-create",
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"name": "MOSuite - create multiOmicDataSet",
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"collect": true
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}
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]
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},
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{
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"name": "capsule_mosuite_filter_low_counts_6",
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"name": "capsule_mosuite_batch_correct_counts_9",
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"capsule": {
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"id": "0296f612-3498-4ed0-ac13-50620e45d67d",
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"name": "MOSuite - filter low counts",
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"slug": "4565215",
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"id": "065804a2-efa7-43f2-9692-967bf0d6b592",
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"name": "MOSuite - batch correct counts",
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"slug": "1373453",
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"version": 1,
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"app_panel": true
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},
@@ -63,20 +109,22 @@
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},
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"inputs": [
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{
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"id": "5mMm7tSyL4NR9Kfo",
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"source_id": "capsule_mosuite_clean_raw_counts_5",
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"id": "dJd8ahCd0Rk0i1Fn",
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"source_id": "capsule_mosuite_normalize_counts_7",
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"type": "capsule",
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"name": "MOSuite-clean",
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"collect": true
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"name": "MOSuite - normalize counts"
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}
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]
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],
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"results": {
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"id": "065804a2-efa7-43f2-9692-967bf0d6b592"
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}
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},
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{
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"name": "capsule_mosuite_normalize_counts_7",
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"name": "capsule_mosuite_differential_expression_analysis_10",
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"capsule": {
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"id": "75561d95-aa78-4140-b64d-ddae5b64fc39",
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"name": "MOSuite - normalize counts",
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"slug": "9169525",
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"id": "03afd79c-bd16-4767-ade0-794d2d6c88bc",
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"name": "MOSuite - differential expression analysis",
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"slug": "6218465",
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"version": 1,
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"app_panel": true
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},
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},
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"inputs": [
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{
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"id": "QU4dCV5IbfyyUbob",
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"id": "JVdSgtWT69Eq2VdQ",
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"source_id": "capsule_mosuite_filter_low_counts_6",
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"type": "capsule",
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"name": "MOSuite - filter low counts",
@@ -95,11 +143,63 @@
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]
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},
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{
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"name": "capsule_mosuite_batch_correct_counts_8",
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"name": "capsule_mosuite_filter_differential_expression_results_11",
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"capsule": {
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"id": "065804a2-efa7-43f2-9692-967bf0d6b592",
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"name": "MOSuite - batch correct counts",
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"slug": "1373453",
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"id": "7fffbb1b-6366-4787-987d-79decf782bf2",
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"name": "MOSuite - filter differential expression results",
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"slug": "5215013",
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"version": 1,
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"app_panel": true
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},
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"resources": {
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"cpus": 1,
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"memory": 8
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},
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"inputs": [
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{
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"id": "fNv19BSRC3Tk0krR",
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"source_id": "capsule_mosuite_differential_expression_analysis_10",
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"type": "capsule",
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"name": "MOSuite - differential expression analysis",
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"collect": true
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}
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],
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"results": {
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"id": "7fffbb1b-6366-4787-987d-79decf782bf2"
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}
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},
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{
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"name": "capsule_mosuite_plot_expression_heatmap_12",
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"capsule": {
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"id": "e9bb1415-3976-46d0-b978-2e8e3554ecd2",
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"name": "MOSuite - plot expression heatmap",
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"slug": "0936928",
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"version": 1,
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"app_panel": true
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},
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"resources": {
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"cpus": 1,
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"memory": 8
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},
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"inputs": [
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{
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"id": "w2iEHre0TvekYCBP",
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"source_id": "capsule_mosuite_normalize_counts_7",
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"type": "capsule",
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"name": "MOSuite - normalize counts",
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"collect": true
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}
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],
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"results": {
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"id": "e9bb1415-3976-46d0-b978-2e8e3554ecd2"
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}
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},
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{
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"name": "capsule_mosuite_plot_2_d_pca_13",
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"capsule": {
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"id": "74b4ec28-63bb-4007-a375-053c8d76260d",
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"name": "MOSuite - plot 2D PCA",
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"slug": "8095429",
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"version": 1,
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"app_panel": true
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},
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},
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"inputs": [
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{
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"id": "0RTvklzjFbQIkCtU",
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"id": "ciBBlF86ihcMUK94",
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"source_id": "capsule_mosuite_normalize_counts_7",
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"type": "capsule",
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"name": "MOSuite - normalize counts",
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"collect": true
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}
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],
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"results": {
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"id": "74b4ec28-63bb-4007-a375-053c8d76260d"
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}
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},
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{
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"name": "capsule_mosuite_plot_3_d_pca_14",
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"capsule": {
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"id": "a160b105-3084-46fc-8cc9-02886fd4bacb",
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"name": "MOSuite - plot 3D PCA",
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"slug": "3838154",
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"app_panel": true
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},
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"resources": {
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"cpus": 1,
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"memory": 8
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},
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"inputs": [
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{
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"id": "PlnhVpRyQ5aCTatd",
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"source_id": "capsule_mosuite_normalize_counts_7",
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"type": "capsule",
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"name": "MOSuite - normalize counts",
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"collect": true
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}
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],
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"results": {
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"id": "2eae5a71-36a6-44e2-a3b2-2cd5634b445d"
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"id": "a160b105-3084-46fc-8cc9-02886fd4bacb"
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}
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}
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]

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