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ro-crate-metadata.json
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ro-crate-metadata.json
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{
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"https://w3id.org/ro/crate/1.1/context",
"https://w3id.org/ro/terms/sapporo",
"https://w3id.org/ro/terms/workflow-run"
],
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{
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},
{
"@id": "https://w3id.org/ro/wfrun/workflow/0.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
],
"datePublished": "2024-07-08T10:25:10+00:00",
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},
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{
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},
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},
{
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},
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},
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},
{
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},
{
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}
],
"license": "https://opensource.org/license/apache-2-0/",
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},
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{
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}
]
},
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
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},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
]
},
{
"@id": "https://w3id.org/ro/wfrun/process/0.1",
"@type": "CreativeWork",
"name": "Process Run Crate",
"version": "0.1"
},
{
"@id": "https://w3id.org/ro/wfrun/workflow/0.1",
"@type": "CreativeWork",
"name": "Workflow Run Crate",
"version": "0.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
"@type": "CreativeWork",
"name": "Workflow RO-Crate",
"version": "1.0"
},
{
"@id": "exe/trimming_and_qc.cwl",
"@type": [
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"SoftwareSourceCode",
"ComputationalWorkflow"
],
"name": "exe/trimming_and_qc",
"programmingLanguage": {
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}
},
{
"@id": "https://w3id.org/cwl/v1.0/",
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"WebPage"
]
},
{
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]
},
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"identifier": {
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},
"name": "Common Workflow Language",
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"name": "Sapporo stderr",
"sha512": "2f3b8e94cccaa9cc138930266b23a1c71387529fd9b19aae78f14e049dc9db3f905914de2b26e096cd2f05c745ffafc239e948cd59c9690a93d9392f1c1298be",
"text": "\u001b[1;30mINFO\u001b[0m /usr/local/bin/cwltool 3.1.20240508115724\n\u001b[1;30mINFO\u001b[0m Resolved 'trimming_and_qc.cwl' to 'file:///home/suecharo/git/github.com/sapporo-wes/sapporo-service/run/b5/b5fbc050-ebad-49d7-97c0-a633f1dfe8bd/exe/trimming_and_qc.cwl'\n\u001b[1;30mINFO\u001b[0m [workflow ] start\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step qc_1\n\u001b[1;30mINFO\u001b[0m [step qc_1] start\n\u001b[1;30mINFO\u001b[0m [job qc_1] /tmp/1ya391fg$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/1ya391fg,target=/tYFKdZ \\\n --mount=type=bind,source=/tmp/87txg70q,target=/tmp \\\n --mount=type=bind,source=/home/suecharo/git/github.com/sapporo-wes/sapporo-service/run/b5/b5fbc050-ebad-49d7-97c0-a633f1dfe8bd/exe/ERR034597_1.small.fq.gz,target=/var/lib/cwl/stgadc9c303-33de-4d06-ba6b-33289124ebc4/ERR034597_1.small.fq.gz,readonly \\\n --workdir=/tYFKdZ \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/i2bdx2sb/20240708102500-468297.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/tYFKdZ \\\n quay.io/biocontainers/fastqc:0.11.9--0 \\\n fastqc \\\n -o \\\n . \\\n --threads \\\n 2 \\\n /var/lib/cwl/stgadc9c303-33de-4d06-ba6b-33289124ebc4/ERR034597_1.small.fq.gz > /tmp/1ya391fg/fastqc-stdout.log 2> /tmp/1ya391fg/fastqc-stderr.log\n\u001b[1;30mINFO\u001b[0m [job qc_1] Max memory used: 151MiB\n\u001b[1;30mINFO\u001b[0m [job qc_1] completed success\n\u001b[1;30mINFO\u001b[0m [step qc_1] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step trimming\n\u001b[1;30mINFO\u001b[0m [step trimming] start\n\u001b[1;30mINFO\u001b[0m [job trimming] /tmp/915m2u86$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/915m2u86,target=/tYFKdZ \\\n --mount=type=bind,source=/tmp/v9ylioin,target=/tmp \\\n --mount=type=bind,source=/home/suecharo/git/github.com/sapporo-wes/sapporo-service/run/b5/b5fbc050-ebad-49d7-97c0-a633f1dfe8bd/exe/ERR034597_1.small.fq.gz,target=/var/lib/cwl/stgcb798aeb-1733-49be-ae0a-5c12f04e643d/ERR034597_1.small.fq.gz,readonly \\\n --mount=type=bind,source=/home/suecharo/git/github.com/sapporo-wes/sapporo-service/run/b5/b5fbc050-ebad-49d7-97c0-a633f1dfe8bd/exe/ERR034597_2.small.fq.gz,target=/var/lib/cwl/stg8905844f-b9c7-47d5-8386-7a2d7e0036cd/ERR034597_2.small.fq.gz,readonly \\\n --workdir=/tYFKdZ \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/i_xohooi/20240708102503-432220.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/tYFKdZ \\\n quay.io/biocontainers/trimmomatic:0.38--1 \\\n trimmomatic \\\n PE \\\n -threads \\\n 2 \\\n /var/lib/cwl/stgcb798aeb-1733-49be-ae0a-5c12f04e643d/ERR034597_1.small.fq.gz \\\n /var/lib/cwl/stg8905844f-b9c7-47d5-8386-7a2d7e0036cd/ERR034597_2.small.fq.gz \\\n ERR034597_1.small.fq.trimmed.1P.fq \\\n ERR034597_1.small.fq.trimmed.1U.fq \\\n ERR034597_1.small.fq.trimmed.2P.fq \\\n ERR034597_1.small.fq.trimmed.2U.fq \\\n ILLUMINACLIP:/usr/local/share/trimmomatic/adapters/TruSeq2-PE.fa:2:40:15 \\\n LEADING:20 \\\n TRAILING:20 \\\n SLIDINGWINDOW:4:15 \\\n MINLEN:36 > /tmp/915m2u86/trimmomatic-pe-stdout.log 2> /tmp/915m2u86/trimmomatic-pe-stderr.log\n\u001b[1;30mINFO\u001b[0m [job trimming] Max memory used: 0MiB\n\u001b[1;30mINFO\u001b[0m [job trimming] completed success\n\u001b[1;30mINFO\u001b[0m [step trimming] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step qc_2\n\u001b[1;30mINFO\u001b[0m [step qc_2] start\n\u001b[1;30mINFO\u001b[0m [job qc_2] /tmp/ljy2q_um$ docker \\\n run \\\n -i \\\n --mount=type=bind,source=/tmp/ljy2q_um,target=/tYFKdZ \\\n --mount=type=bind,source=/tmp/ai5jjrkt,target=/tmp \\\n --mount=type=bind,source=/home/suecharo/git/github.com/sapporo-wes/sapporo-service/run/b5/b5fbc050-ebad-49d7-97c0-a633f1dfe8bd/exe/ERR034597_2.small.fq.gz,target=/var/lib/cwl/stg042f7daa-c0e2-4451-a358-851b26440a70/ERR034597_2.small.fq.gz,readonly \\\n --workdir=/tYFKdZ \\\n --read-only=true \\\n --log-driver=none \\\n --user=0:0 \\\n --rm \\\n --cidfile=/tmp/5rziihf7/20240708102504-787813.cid \\\n --env=TMPDIR=/tmp \\\n --env=HOME=/tYFKdZ \\\n quay.io/biocontainers/fastqc:0.11.9--0 \\\n fastqc \\\n -o \\\n . \\\n --threads \\\n 2 \\\n /var/lib/cwl/stg042f7daa-c0e2-4451-a358-851b26440a70/ERR034597_2.small.fq.gz > /tmp/ljy2q_um/fastqc-stdout.log 2> /tmp/ljy2q_um/fastqc-stderr.log\n\u001b[1;30mINFO\u001b[0m [job qc_2] Max memory used: 173MiB\n\u001b[1;30mINFO\u001b[0m [job qc_2] completed success\n\u001b[1;30mINFO\u001b[0m [step qc_2] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] completed success\n\u001b[1;30mINFO\u001b[0m Final process status is success\n"
}
]
}