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Fastqc#489

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acashmoney merged 3 commits intolabdao:mainfrom
flowscience:fastqc
Jul 13, 2023
Merged

Fastqc#489
acashmoney merged 3 commits intolabdao:mainfrom
flowscience:fastqc

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vercel bot commented Jul 12, 2023

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Thanks @flowscience, approved! I made a small change to move the testdata you provided into a dedicated folder. It's now at plex/testdata/sequencing/fastqc/testdata.fastq.

Run

./plex create -t tools/fastqc/fastqc.json -i testdata/sequencing/fastqc --autoRun=true
Plex version (v0.8.3) up to date.
Temporary directory created: /var/folders/v3/nwpptsrj2wx7rddqg0wd33rr0000gn/T/b52e711f-e966-48a7-97b4-e3a9b470fb944268966443
Reading tool config:  tools/fastqc/fastqc.json
Creating IO entries from input directory:  testdata/sequencing/fastqc
Initialized IO file at:  /var/folders/v3/nwpptsrj2wx7rddqg0wd33rr0000gn/T/b52e711f-e966-48a7-97b4-e3a9b470fb944268966443/io.json
Initial IO JSON file CID:  QmeLbEWFvY9xCF2CmWqntE5STpiW4DwEoCpLWXFd9k9tQF
Created working directory:  /Users/aakaash/Desktop/code/OPENLAB/temp/plex/jobs/dddb0066-f86f-46db-8884-0248ce514156
Initialized IO file at:  /Users/aakaash/Desktop/code/OPENLAB/temp/plex/jobs/dddb0066-f86f-46db-8884-0248ce514156/io.json
Processing IO Entries
Starting to process IO entry 0
Job running...
Bacalhau job id: 0a939133-87fe-4348-841d-c48cd54c3f74
////_🌱___////
Computing default go-libp2p Resource Manager limits based on:
    - 'Swarm.ResourceMgr.MaxMemory': "8.6 GB"
    - 'Swarm.ResourceMgr.MaxFileDescriptors': 30720

Applying any user-supplied overrides on top.
Run 'ipfs swarm limit all' to see the resulting limits.

Success processing IO entry 0
Finished processing, results written to /Users/aakaash/Desktop/code/OPENLAB/temp/plex/jobs/dddb0066-f86f-46db-8884-0248ce514156/io.json
Completed IO JSON CID: QmXQ4fh9aZL6bUXZMDXLW4U7Wyv6A6rgFLN99XVBSsTGB2

Results

[
    {
        "outputs": {
            "outdata": {
                "class": "File",
                "filepath": "testdata_fastqc.zip",
                "ipfs": "QmV81EZWRuu3HhK8aZxsvj7XpZEeHVjABKwZJ52XRxsnki"
            },
            "report": {
                "class": "File",
                "filepath": "testdata_fastqc.html",
                "ipfs": "QmbdDa4SpMbmCFwsshRws1Ek2DPe9QPiGXFu32MQLuwhYY"
            }
        },
        "tool": {
            "name": "fastqc",
            "ipfs": "QmdJhaeDUAiR5VdSyREwv2Hz7fnidMYRQQZ5Cus4cV3pjz"
        },
        "inputs": {
            "reads": {
                "class": "File",
                "filepath": "testdata.fastq",
                "ipfs": "QmUvALPCVL5ZgnRWyvfqjrTSK9UgLW1JJTLsisFooRpcGD"
            }
        },
        "state": "completed",
        "errMsg": ""
    }
]
Screenshot 2023-07-13 at 1 29 35 PM

@acashmoney acashmoney merged commit 05455db into labdao:main Jul 13, 2023
@acashmoney acashmoney mentioned this pull request Jul 13, 2023
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2 participants