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bacass-dirt02-001.json
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{
"name": "bacass",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-29T20:02:41.814660+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/bacass",
"runName": "cheesy_gautier",
"executedAt": "2023-03-29T10:02:36-10:00",
"tasks": [
{
"name": "NFCORE_BACASS.BACASS.FASTQC",
"id": "2",
"type": "compute",
"command": {
"program": "[ ! -f ERR044595_1.fastq.gz ] && ln -s ERR044595_1M_1.fastq.gz ERR044595_1.fastq.gz\n [ ! -f ERR044595_2.fastq.gz ] && ln -s ERR044595_1M_2.fastq.gz ERR044595_2.fastq.gz\n fastqc --quiet --threads 1 ERR044595_1.fastq.gz ERR044595_2.fastq.gz\n fastqc --version | sed -e \"s/FastQC v//g\" > fastqc.version.txt",
"arguments": []
},
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"path": "/nf-core/test-datasets/raw/bacass/",
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"name": "ERR044595_1_fastqc.zip",
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"link": "output",
"name": "ERR044595_2_fastqc.zip",
"path": "/b6/e95c72d7ef9da13b7641118999df15/",
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},
{
"name": "NFCORE_BACASS.BACASS.SKEWER",
"id": "1",
"type": "compute",
"command": {
"program": "# loop over readunits in pairs per sample\n pairno=0\n echo \"ERR044595_1M_1.fastq.gz ERR044595_1M_2.fastq.gz\" | xargs -n2 | while read fq1 fq2; do\n skewer -m pe -q 3 -n --quiet -t 1 $fq1 $fq2;\n done\n\n # gzip, because skewer's -z returns an error\n gzip *.fastq\n\n cat $(ls *trimmed-pair1.fastq.gz | sort) >> ERR044595_trm-cmb.R1.fastq.gz\n cat $(ls *trimmed-pair2.fastq.gz | sort) >> ERR044595_trm-cmb.R2.fastq.gz\n\n echo $(skewer --version 2>&1) | sed 's/^.*skewer version: //; s/ .*//' > skewer.version.txt",
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"link": "output",
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"path": "/3d/7a64449bc37c576aba41bbd65e7f04/",
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"readBytes": 1055485017,
"runtimeInSeconds": 208.0
},
{
"name": "NFCORE_BACASS.BACASS.FASTQC",
"id": "4",
"type": "compute",
"command": {
"program": "[ ! -f ERR064912_1.fastq.gz ] && ln -s ERR064912_1M_1.fastq.gz ERR064912_1.fastq.gz\n [ ! -f ERR064912_2.fastq.gz ] && ln -s ERR064912_1M_2.fastq.gz ERR064912_2.fastq.gz\n fastqc --quiet --threads 1 ERR064912_1.fastq.gz ERR064912_2.fastq.gz\n fastqc --version | sed -e \"s/FastQC v//g\" > fastqc.version.txt",
"arguments": []
},
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"name": "ERR064912_1M_1.fastq.gz",
"path": "/nf-core/test-datasets/raw/bacass/",
"sizeInBytes": 53691898
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{
"link": "input",
"name": "ERR064912_1M_2.fastq.gz",
"path": "/nf-core/test-datasets/raw/bacass/",
"sizeInBytes": 56303947
},
{
"link": "output",
"name": "ERR064912_1_fastqc.html",
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"link": "output",
"name": "ERR064912_2_fastqc.html",
"path": "/ff/4f4c6dcc93a320dd39a720fe5e90a2/",
"sizeInBytes": 715345
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{
"link": "output",
"name": "ERR064912_1_fastqc.zip",
"path": "/ff/4f4c6dcc93a320dd39a720fe5e90a2/",
"sizeInBytes": 404152
},
{
"link": "output",
"name": "ERR064912_2_fastqc.zip",
"path": "/ff/4f4c6dcc93a320dd39a720fe5e90a2/",
"sizeInBytes": 395393
},
{
"link": "output",
"name": "fastqc.version.txt",
"path": "/ff/4f4c6dcc93a320dd39a720fe5e90a2/",
"sizeInBytes": 7
}
],
"avgCPU": 87.9,
"inputFilesBytes": 109995845,
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"writtenBytes": 4349821,
"readBytes": 132095919,
"runtimeInSeconds": 37.0
},
{
"name": "NFCORE_BACASS.BACASS.SKEWER",
"id": "3",
"type": "compute",
"command": {
"program": "# loop over readunits in pairs per sample\n pairno=0\n echo \"ERR064912_1M_1.fastq.gz ERR064912_1M_2.fastq.gz\" | xargs -n2 | while read fq1 fq2; do\n skewer -m pe -q 3 -n --quiet -t 1 $fq1 $fq2;\n done\n\n # gzip, because skewer's -z returns an error\n gzip *.fastq\n\n cat $(ls *trimmed-pair1.fastq.gz | sort) >> ERR064912_trm-cmb.R1.fastq.gz\n cat $(ls *trimmed-pair2.fastq.gz | sort) >> ERR064912_trm-cmb.R2.fastq.gz\n\n echo $(skewer --version 2>&1) | sed 's/^.*skewer version: //; s/ .*//' > skewer.version.txt",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "ERR064912_1M_1.fastq.gz",
"path": "/nf-core/test-datasets/raw/bacass/",
"sizeInBytes": 53691898
},
{
"link": "input",
"name": "ERR064912_1M_2.fastq.gz",
"path": "/nf-core/test-datasets/raw/bacass/",
"sizeInBytes": 56303947
},
{
"link": "output",
"name": "ERR064912_trm-cmb.R1.fastq.gz",
"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
"sizeInBytes": 52163305
},
{
"link": "output",
"name": "ERR064912_trm-cmb.R2.fastq.gz",
"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
"sizeInBytes": 54778579
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{
"link": "output",
"name": "ERR064912_1M_1.fastq-trimmed.log",
"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
"sizeInBytes": 1769
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{
"link": "output",
"name": "skewer.version.txt",
"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
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"memoryInBytes": 9314304,
"writtenBytes": 1035059815,
"readBytes": 1038199623,
"runtimeInSeconds": 192.0
},
{
"name": "NFCORE_BACASS.BACASS.UNICYCLER",
"id": "5",
"type": "compute",
"command": {
"program": "unicycler \\\n --threads 1 \\\n --no_correct --no_pilon \\\n -1 ERR044595_trm-cmb.R1.fastq.gz -2 ERR044595_trm-cmb.R2.fastq.gz \\\n --out ./\n\n mv assembly.fasta ERR044595.scaffolds.fa\n mv assembly.gfa ERR044595.assembly.gfa\n mv unicycler.log ERR044595.unicycler.log\n\n echo $(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*$//' > unicycler.version.txt",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "ERR044595_trm-cmb.R1.fastq.gz",
"path": "/3d/7a64449bc37c576aba41bbd65e7f04/",
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},
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"link": "input",
"name": "ERR044595_trm-cmb.R2.fastq.gz",
"path": "/3d/7a64449bc37c576aba41bbd65e7f04/",
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},
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"link": "output",
"name": "ERR044595.scaffolds.fa",
"path": "/6f/1e54d3680877daf943e956e3dd66fb/",
"sizeInBytes": 2820746
},
{
"link": "output",
"name": "ERR044595.assembly.gfa",
"path": "/6f/1e54d3680877daf943e956e3dd66fb/",
"sizeInBytes": 2797122
},
{
"link": "output",
"name": "ERR044595.unicycler.log",
"path": "/6f/1e54d3680877daf943e956e3dd66fb/",
"sizeInBytes": 17474
},
{
"link": "output",
"name": "unicycler.version.txt",
"path": "/6f/1e54d3680877daf943e956e3dd66fb/",
"sizeInBytes": 6
}
],
"avgCPU": 95.3,
"inputFilesBytes": 113502236,
"outputFilesBytes": 5635348,
"memoryInBytes": 1112813568,
"writtenBytes": 10321983523,
"readBytes": 3839067195,
"runtimeInSeconds": 949.0
},
{
"name": "NFCORE_BACASS.BACASS.UNICYCLER",
"id": "6",
"type": "compute",
"command": {
"program": "unicycler \\\n --threads 1 \\\n --no_correct --no_pilon \\\n -1 ERR064912_trm-cmb.R1.fastq.gz -2 ERR064912_trm-cmb.R2.fastq.gz \\\n --out ./\n\n mv assembly.fasta ERR064912.scaffolds.fa\n mv assembly.gfa ERR064912.assembly.gfa\n mv unicycler.log ERR064912.unicycler.log\n\n echo $(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*$//' > unicycler.version.txt",
"arguments": []
},
"parents": [],
"children": [],
"files": [
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"link": "input",
"name": "ERR064912_trm-cmb.R1.fastq.gz",
"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
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"link": "input",
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"path": "/17/2ebf9cc4b87470e9a57c9b7042576e/",
"sizeInBytes": 54778579
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"link": "output",
"name": "ERR064912.scaffolds.fa",
"path": "/bb/09067ce6b0622cfdce89f8e324f710/",
"sizeInBytes": 2955111
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{
"link": "output",
"name": "ERR064912.assembly.gfa",
"path": "/bb/09067ce6b0622cfdce89f8e324f710/",
"sizeInBytes": 2940497
},
{
"link": "output",
"name": "ERR064912.unicycler.log",
"path": "/bb/09067ce6b0622cfdce89f8e324f710/",
"sizeInBytes": 16817
},
{
"link": "output",
"name": "unicycler.version.txt",
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"readBytes": 3841079174,
"runtimeInSeconds": 1385.0
},
{
"name": "NFCORE_BACASS.BACASS.PROKKA",
"id": "7",
"type": "compute",
"command": {
"program": "prokka \\\n --fast \\\n --cpus 1 \\\n --prefix ERR044595 \\\n \\\n \\\n ERR044595.scaffolds.fa\n\n echo $(prokka --version 2>&1) | sed 's/^.*prokka //' > prokka.version.txt",
"arguments": []
},
"parents": [],
"children": [],
"files": [
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"link": "input",
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"path": "/6f/1e54d3680877daf943e956e3dd66fb/",
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