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taxprofiler-dirt02-001.json
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{
"name": "taxprofiler",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-29T17:15:25.610327+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/taxprofiler",
"runName": "drunk_franklin",
"executedAt": "2023-03-29T07:15:18-10:00",
"tasks": [
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.INPUT_CHECK.SAMPLESHEET_CHECK",
"id": "2",
"type": "compute",
"command": {
"program": "check_samplesheet.py \\\n samplesheet.csv \\\n samplesheet.valid.csv\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK\":\n python: $(python --version | sed 's/Python //g')\n END_VERSIONS",
"arguments": []
},
"parents": [],
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{
"link": "input",
"name": "samplesheet.csv",
"path": "/nf-core/test-datasets/taxprofiler/",
"sizeInBytes": 1233
},
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"link": "output",
"name": "samplesheet.valid.csv",
"path": "/6d/60f703c6b92cc74f55f6ffae18faa1/",
"sizeInBytes": 1256
},
{
"link": "output",
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}
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"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.SHORTREAD_HOSTREMOVAL.BOWTIE2_BUILD",
"id": "3",
"type": "compute",
"command": {
"program": "mkdir bowtie2\n bowtie2-build --threads 1 genome.fasta bowtie2/genome\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:BOWTIE2_BUILD\":\n bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "genome.fasta",
"path": "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/",
"sizeInBytes": 40675
},
{
"link": "output",
"name": "bowtie2",
"path": "/f0/52d35614f7de6164d5b11258989005/",
"sizeInBytes": 8445728
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},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.LONGREAD_HOSTREMOVAL.MINIMAP2_INDEX",
"id": "1",
"type": "compute",
"command": {
"program": "minimap2 \\\n -t 1 \\\n -d genome.mmi \\\n -x map-ont \\\n genome.fasta\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:LONGREAD_HOSTREMOVAL:MINIMAP2_INDEX\":\n minimap2: $(minimap2 --version 2>&1)\n END_VERSIONS",
"arguments": []
},
"parents": [],
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},
{
"link": "output",
"name": "genome.mmi",
"path": "/37/a53d1f5b44bde722eea61f1d1134e8/",
"sizeInBytes": 270726
},
{
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}
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},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.DB_CHECK.UNTAR",
"id": "4",
"type": "compute",
"command": {
"program": "mkdir output\n\n ## Ensures --strip-components only applied when top level of tar contents is a directory\n ## If just files or multiple directories, place all in output\n if [[ $(tar -tzf testdb-bracken.tar.gz | grep -o -P \"^.*?\\/\" | uniq | wc -l) -eq 1 ]]; then\n tar \\\n -C output --strip-components 1 \\\n -xzvf \\\n \\\n testdb-bracken.tar.gz \\\n \n else\n tar \\\n -C output \\\n -xzvf \\\n \\\n testdb-bracken.tar.gz \\\n \n fi\n\n mv output testdb-bracken\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR\":\n untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "testdb-bracken.tar.gz",
"path": "/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/",
"sizeInBytes": 14424948
},
{
"link": "output",
"name": "testdb-bracken",
"path": "/7e/1c6cba3473c99b51390dfb32ee580a/",
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},
{
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"name": "versions.yml",
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}
],
"avgCPU": 55.3,
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"runtimeInSeconds": 0.834
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.DB_CHECK.UNTAR",
"id": "7",
"type": "compute",
"command": {
"program": "mkdir output\n\n ## Ensures --strip-components only applied when top level of tar contents is a directory\n ## If just files or multiple directories, place all in output\n if [[ $(tar -tzf metaphlan_database.tar.gz | grep -o -P \"^.*?\\/\" | uniq | wc -l) -eq 1 ]]; then\n tar \\\n -C output --strip-components 1 \\\n -xzvf \\\n \\\n metaphlan_database.tar.gz \\\n \n else\n tar \\\n -C output \\\n -xzvf \\\n \\\n metaphlan_database.tar.gz \\\n \n fi\n\n mv output metaphlan_database\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR\":\n untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
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"path": "/nf-core/test-datasets/modules/data/delete_me/",
"sizeInBytes": 23881
},
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"name": "metaphlan_database",
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"sizeInBytes": 8421490
},
{
"link": "output",
"name": "versions.yml",
"path": "/78/656cd85c82d8647b81e73cc38b314e/",
"sizeInBytes": 65
}
],
"avgCPU": 80.8,
"inputFilesBytes": 23881,
"outputFilesBytes": 8421555,
"memoryInBytes": 2953216,
"writtenBytes": 25298995,
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"runtimeInSeconds": 0.158
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.DB_CHECK.UNTAR",
"id": "5",
"type": "compute",
"command": {
"program": "mkdir output\n\n ## Ensures --strip-components only applied when top level of tar contents is a directory\n ## If just files or multiple directories, place all in output\n if [[ $(tar -tzf testdb-kraken2.tar.gz | grep -o -P \"^.*?\\/\" | uniq | wc -l) -eq 1 ]]; then\n tar \\\n -C output --strip-components 1 \\\n -xzvf \\\n \\\n testdb-kraken2.tar.gz \\\n \n else\n tar \\\n -C output \\\n -xzvf \\\n \\\n testdb-kraken2.tar.gz \\\n \n fi\n\n mv output testdb-kraken2\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR\":\n untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "testdb-kraken2.tar.gz",
"path": "/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/",
"sizeInBytes": 14373328
},
{
"link": "output",
"name": "testdb-kraken2",
"path": "/7d/3be2a914527e743f3c8001b403ddeb/",
"sizeInBytes": 20392840
},
{
"link": "output",
"name": "versions.yml",
"path": "/7d/3be2a914527e743f3c8001b403ddeb/",
"sizeInBytes": 65
}
],
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"writtenBytes": 61190209,
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"runtimeInSeconds": 0.856
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.DB_CHECK.UNTAR",
"id": "6",
"type": "compute",
"command": {
"program": "mkdir output\n\n ## Ensures --strip-components only applied when top level of tar contents is a directory\n ## If just files or multiple directories, place all in output\n if [[ $(tar -tzf test-db-centrifuge.tar.gz | grep -o -P \"^.*?\\/\" | uniq | wc -l) -eq 1 ]]; then\n tar \\\n -C output --strip-components 1 \\\n -xzvf \\\n \\\n test-db-centrifuge.tar.gz \\\n \n else\n tar \\\n -C output \\\n -xzvf \\\n \\\n test-db-centrifuge.tar.gz \\\n \n fi\n\n mv output test-db-centrifuge\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR\":\n untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "test-db-centrifuge.tar.gz",
"path": "/nf-core/test-datasets/raw/taxprofiler/data/database/centrifuge/",
"sizeInBytes": 5506932
},
{
"link": "output",
"name": "test-db-centrifuge",
"path": "/c4/0776298cd5bacfcef65b53694e6545/",
"sizeInBytes": 13973070
},
{
"link": "output",
"name": "versions.yml",
"path": "/c4/0776298cd5bacfcef65b53694e6545/",
"sizeInBytes": 65
}
],
"avgCPU": 50.7,
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"writtenBytes": 41950183,
"readBytes": 39149173,
"runtimeInSeconds": 0.651
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.DB_CHECK.UNTAR",
"id": "8",
"type": "compute",
"command": {
"program": "mkdir output\n\n ## Ensures --strip-components only applied when top level of tar contents is a directory\n ## If just files or multiple directories, place all in output\n if [[ $(tar -tzf kaiju.tar.gz | grep -o -P \"^.*?\\/\" | uniq | wc -l) -eq 1 ]]; then\n tar \\\n -C output --strip-components 1 \\\n -xzvf \\\n \\\n kaiju.tar.gz \\\n \n else\n tar \\\n -C output \\\n -xzvf \\\n \\\n kaiju.tar.gz \\\n \n fi\n\n mv output kaiju\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR\":\n untar: $(echo $(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "kaiju.tar.gz",
"path": "/nf-core/test-datasets/raw/taxprofiler/data/database/kaiju/",
"sizeInBytes": 10160
},
{
"link": "output",
"name": "kaiju",
"path": "/f7/d411ef4541d8687998081ea0bcd493/",
"sizeInBytes": 12773
},
{
"link": "output",
"name": "versions.yml",
"path": "/f7/d411ef4541d8687998081ea0bcd493/",
"sizeInBytes": 65
}
],
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"memoryInBytes": 2985984,
"writtenBytes": 59005,
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"runtimeInSeconds": 0.053
},
{
"name": "NFCORE_TAXPROFILER.TAXPROFILER.FASTQC",
"id": "10",
"type": "compute",
"command": {
"program": "printf \"%s %s\\n\" ERR3201952.fastq.gz ERR3201952_ERR3201952_raw.gz | while read old_name new_name; do\n [ -f \"${new_name}\" ] || ln -s $old_name $new_name\n done\n fastqc --quiet --threads 1 ERR3201952_ERR3201952_raw.gz\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:FASTQC\":\n fastqc: $( fastqc --version | sed -e \"s/FastQC v//g\" )\n END_VERSIONS",
"arguments": []
},
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"link": "input",
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"link": "input",
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"link": "input",
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"name": "NFCORE_TAXPROFILER.TAXPROFILER.SHORTREAD_PREPROCESSING.SHORTREAD_FASTP.FASTP_PAIRED",
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"command": {
"program": "[ ! -f 2613_ERR5766181_1.fastq.gz ] && ln -sf ERX5474937_ERR5766181_1.fastq.gz 2613_ERR5766181_1.fastq.gz\n [ ! -f 2613_ERR5766181_2.fastq.gz ] && ln -sf ERX5474937_ERR5766181_2.fastq.gz 2613_ERR5766181_2.fastq.gz\n fastp \\\n --in1 2613_ERR5766181_1.fastq.gz \\\n --in2 2613_ERR5766181_2.fastq.gz \\\n --out1 2613_ERR5766181_1.fastp.fastq.gz \\\n --out2 2613_ERR5766181_2.fastp.fastq.gz \\\n --json 2613_ERR5766181.fastp.json \\\n --html 2613_ERR5766181.fastp.html \\\n \\\n \\\n -m --merged_out 2613_ERR5766181.merged.fastq.gz \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --detect_adapter_for_pe --length_required 15 \\\n 2> 2613_ERR5766181.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_PREPROCESSING:SHORTREAD_FASTP:FASTP_PAIRED\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
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},
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