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‎.codeocean/app-panel.json‎

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{
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"version": 1,
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"processes": [
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"capsule_mosuite_create_2"
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]
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}

‎.codeocean/nextflow.json‎

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{
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"version": 2,
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"processes": [
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{
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"name": "capsule_mosuite_clean_1",
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"capsule": {
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"id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b",
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"name": "MOSuite-clean",
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"slug": "5801113",
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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": "uqbFE30XQBTDxBxR",
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"source_id": "capsule_mosuite_create_2",
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"type": "capsule",
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"name": "MOSuite-create"
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}
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]
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},
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{
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"name": "capsule_mosuite_create_2",
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"capsule": {
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"id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030",
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"name": "MOSuite-create",
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"slug": "6541445",
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"version": 2,
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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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}
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]
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}

‎.codeocean/pipeline-layout.json‎

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{
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"edges": [
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{
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"id": "xy-edge__capsule_mosuite_create_2-capsule_mosuite_clean_1",
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"source": "capsule_mosuite_create_2",
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"target": "capsule_mosuite_clean_1"
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}
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],
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"nodes": [
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{
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"data": {
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"capsule_id": "ab07963e-d9e0-489e-b776-70f6ef2ef73b"
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},
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"id": "capsule_mosuite_clean_1",
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"position": {
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"x": 842.6666666666667,
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"y": 270
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},
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"selected": false,
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"type": "capsule"
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},
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{
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"id": "results",
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"position": {
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"x": 960,
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"y": 614
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},
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"type": "results"
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},
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{
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"data": {
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"capsule_id": "5ce5f88d-980d-4e61-b3a4-ef4a0ce48030"
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},
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"id": "capsule_mosuite_create_2",
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"position": {
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"x": 718.6666666666666,
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"y": 31.333333333333343
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},
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"selected": true,
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"type": "capsule"
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}
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],
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"timestamp": 1769554760195,
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"viewport": {
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"x": 6,
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"y": 87,
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"zoom": 0.75
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}
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}

‎.codeocean/settings.json‎

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{
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"version": 1,
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"nextflow_version": "24.10.4",
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"verbose_logs": true
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}

‎.gitignore‎

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/data/

‎metadata/metadata.yml‎

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metadata_version: 1
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name: MOSuite-pipeline
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description: MOSuite pipeline for differential analysis of multi-omic data
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tags:
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- Bulk RNA-seq
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- MOSuite
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authors:
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- name: CCR Collaborative Bioinformatics Resource
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- name: Kelly Sovacool

‎pipeline/main.nf‎

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#!/usr/bin/env nextflow
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// hash:sha256:e60c74eb0db9870da170bd3833dbe435cba6b383333fc48223204b0a17b1e6f0
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// capsule - MOSuite-create
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process capsule_mosuite_create_2 {
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tag 'capsule-6541445'
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container "$REGISTRY_HOST/published/5ce5f88d-980d-4e61-b3a4-ef4a0ce48030:v2"
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cpus 1
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memory '7.5 GB'
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output:
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path 'capsule/results/*', emit: to_capsule_mosuite_clean_1_1
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script:
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"""
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#!/usr/bin/env bash
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set -e
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export CO_CAPSULE_ID=5ce5f88d-980d-4e61-b3a4-ef4a0ce48030
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export CO_CPUS=1
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export CO_MEMORY=8053063680
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mkdir -p capsule
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mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
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mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
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mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git clone --filter=tree:0 --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
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else
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git clone --branch v2.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-6541445.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo
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echo "[${task.tag}] running capsule..."
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cd capsule/code
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chmod +x run
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./run ${params.capsule_mosuite_create_2_args}
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echo "[${task.tag}] completed!"
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"""
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}
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// capsule - MOSuite-clean
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process capsule_mosuite_clean_1 {
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tag 'capsule-5801113'
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container "$REGISTRY_HOST/published/ab07963e-d9e0-489e-b776-70f6ef2ef73b:v1"
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cpus 1
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memory '7.5 GB'
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input:
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path 'capsule/data/'
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script:
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"""
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#!/usr/bin/env bash
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set -e
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export CO_CAPSULE_ID=ab07963e-d9e0-489e-b776-70f6ef2ef73b
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export CO_CPUS=1
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export CO_MEMORY=8053063680
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mkdir -p capsule
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mkdir -p capsule/data && ln -s \$PWD/capsule/data /data
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mkdir -p capsule/results && ln -s \$PWD/capsule/results /results
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mkdir -p capsule/scratch && ln -s \$PWD/capsule/scratch /scratch
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git clone --filter=tree:0 --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
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else
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git clone --branch v1.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-5801113.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo
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echo "[${task.tag}] running capsule..."
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cd capsule/code
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chmod +x run
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./run ${params.capsule_mosuite_clean_1_args}
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echo "[${task.tag}] completed!"
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"""
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}
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workflow {
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// run processes
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capsule_mosuite_create_2()
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capsule_mosuite_clean_1(capsule_mosuite_create_2.out.to_capsule_mosuite_clean_1_1)
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}

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