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smrnaseq-dirt02-001.json
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smrnaseq-dirt02-001.json
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{
"name": "smrnaseq",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-28T23:10:58.467697+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/smrnaseq",
"runName": "fervent_shockley",
"executedAt": "2023-03-28T13:10:49-10:00",
"tasks": [
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.INPUT_CHECK.SAMPLESHEET_CHECK",
"id": "1",
"type": "compute",
"command": {
"program": "check_samplesheet.py \\\n samplesheet.csv \\\n samplesheet.valid.csv\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ: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/raw/smrnaseq/samplesheet/v2.0/",
"sizeInBytes": 661
},
{
"link": "output",
"name": "samplesheet.valid.csv",
"path": "/89/bcf078f4ff583b4632252846835abb/",
"sizeInBytes": 715
},
{
"link": "output",
"name": "versions.yml",
"path": "/89/bcf078f4ff583b4632252846835abb/",
"sizeInBytes": 76
}
],
"avgCPU": 22.3,
"inputFilesBytes": 661,
"outputFilesBytes": 790,
"memoryInBytes": 3420160,
"writtenBytes": 1102,
"readBytes": 670498,
"runtimeInSeconds": 0.0
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.PARSE_MATURE",
"id": "2",
"type": "compute",
"command": {
"program": "# Uncompress FASTA reference files if necessary\n FASTA=\"mature.fa\"\n if [ ${FASTA: -3} == \".gz\" ]; then\n gunzip -f $FASTA\n FASTA=${FASTA%%.gz}\n fi\n # Remove spaces from miRBase FASTA files\n # sed -i 's, ,_,g' $FASTA\n sed '/^[^>]/s/[^AUGCaugc]/N/g' $FASTA > ${FASTA}_parsed.fa\n # TODO perl -ane 's/[ybkmrsw]/N/ig;print;' ${FASTA}_parsed_tmp.fa > ${FASTA}_parsed.fa\n\n sed -i 's/ .*//' ${FASTA}_parsed.fa\n seqkit grep -r --pattern \".*hsa-.*\" ${FASTA}_parsed.fa > ${FASTA}_sps.fa\n seqkit seq --rna2dna ${FASTA}_sps.fa > ${FASTA}_igenome.fa\n\n cat <<-END_VERSIONS > versions.yml\n NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE\":\n seqkit: $(echo $(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "mature.fa",
"path": "/nf-core/test-datasets/raw/smrnaseq/reference/",
"sizeInBytes": 194966
},
{
"link": "output",
"name": "mature.fa_igenome.fa",
"path": "/9b/cc81f35e2a7ef2ba27997096b4c473/",
"sizeInBytes": 99538
},
{
"link": "output",
"name": "versions.yml",
"path": "/9b/cc81f35e2a7ef2ba27997096b4c473/",
"sizeInBytes": 70
}
],
"avgCPU": 78.5,
"inputFilesBytes": 194966,
"outputFilesBytes": 99607,
"memoryInBytes": 3141632,
"writtenBytes": 502710,
"readBytes": 665387,
"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.PARSE_HAIRPIN",
"id": "3",
"type": "compute",
"command": {
"program": "# Uncompress FASTA reference files if necessary\n FASTA=\"hairpin.fa\"\n if [ ${FASTA: -3} == \".gz\" ]; then\n gunzip -f $FASTA\n FASTA=${FASTA%%.gz}\n fi\n # Remove spaces from miRBase FASTA files\n # sed -i 's, ,_,g' $FASTA\n sed '/^[^>]/s/[^AUGCaugc]/N/g' $FASTA > ${FASTA}_parsed.fa\n # TODO perl -ane 's/[ybkmrsw]/N/ig;print;' ${FASTA}_parsed_tmp.fa > ${FASTA}_parsed.fa\n\n sed -i 's/ .*//' ${FASTA}_parsed.fa\n seqkit grep -r --pattern \".*hsa-.*\" ${FASTA}_parsed.fa > ${FASTA}_sps.fa\n seqkit seq --rna2dna ${FASTA}_sps.fa > ${FASTA}_igenome.fa\n\n cat <<-END_VERSIONS > versions.yml\n NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN\":\n seqkit: $(echo $(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "hairpin.fa",
"path": "/nf-core/test-datasets/raw/smrnaseq/reference/",
"sizeInBytes": 263526
},
{
"link": "output",
"name": "hairpin.fa_igenome.fa",
"path": "/5d/be55062551ddfe848870ff93f4d1de/",
"sizeInBytes": 184264
},
{
"link": "output",
"name": "versions.yml",
"path": "/5d/be55062551ddfe848870ff93f4d1de/",
"sizeInBytes": 71
}
],
"avgCPU": 73.7,
"inputFilesBytes": 263526,
"outputFilesBytes": 184335,
"memoryInBytes": 3158016,
"writtenBytes": 825441,
"readBytes": 971955,
"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.GENOME_QUANT.INDEX_GENOME",
"id": "4",
"type": "compute",
"command": {
"program": "# Remove any special base characters from reference genome FASTA file\n sed '/^[^>]/s/[^ATGCatgc]/N/g' genome.fa > genome.edited.fa\n sed -i 's/ .*//' genome.edited.fa\n\n # Build bowtie index\n bowtie-build genome.edited.fa genome --threads 1\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME\":\n bowtie: $(echo $(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "genome.fa",
"path": "/nf-core/test-datasets/raw/smrnaseq/reference/",
"sizeInBytes": 2587395
},
{
"link": "output",
"name": "genome.1.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 4919231
},
{
"link": "output",
"name": "genome.2.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 317076
},
{
"link": "output",
"name": "genome.3.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 26
},
{
"link": "output",
"name": "genome.4.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 634143
},
{
"link": "output",
"name": "genome.rev.1.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 4919231
},
{
"link": "output",
"name": "genome.rev.2.ebwt",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 317076
},
{
"link": "output",
"name": "genome.edited.fa",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 2587321
},
{
"link": "output",
"name": "versions.yml",
"path": "/92/e8feb908de036b49f5ea1b3be27fa7/",
"sizeInBytes": 72
}
],
"avgCPU": 82.5,
"inputFilesBytes": 2587395,
"outputFilesBytes": 13694176,
"memoryInBytes": 19582976,
"writtenBytes": 16295810,
"readBytes": 17197367,
"runtimeInSeconds": 4.0
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.FORMAT_MATURE",
"id": "5",
"type": "compute",
"command": {
"program": "fasta_formatter -w 0 -i mature.fa_igenome.fa -o mature.fa_igenome.fa_idx.fa\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE\":\n fastx_toolkit: $(echo \"0.0.14\")\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "mature.fa_igenome.fa",
"path": "/9b/cc81f35e2a7ef2ba27997096b4c473/",
"sizeInBytes": 99538
},
{
"link": "output",
"name": "mature.fa_igenome.fa_idx.fa",
"path": "/78/1eb176d18d15ba96f9cff9c1678bd7/",
"sizeInBytes": 99538
},
{
"link": "output",
"name": "versions.yml",
"path": "/78/1eb176d18d15ba96f9cff9c1678bd7/",
"sizeInBytes": 81
}
],
"avgCPU": 23.0,
"inputFilesBytes": 99538,
"outputFilesBytes": 99619,
"memoryInBytes": 3854336,
"writtenBytes": 99922,
"readBytes": 150719,
"runtimeInSeconds": 0.198
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.FORMAT_HAIRPIN",
"id": "6",
"type": "compute",
"command": {
"program": "fasta_formatter -w 0 -i hairpin.fa_igenome.fa -o hairpin.fa_igenome.fa_idx.fa\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN\":\n fastx_toolkit: $(echo \"0.0.14\")\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "hairpin.fa_igenome.fa",
"path": "/5d/be55062551ddfe848870ff93f4d1de/",
"sizeInBytes": 184264
},
{
"link": "output",
"name": "hairpin.fa_igenome.fa_idx.fa",
"path": "/89/082dfcf443ca9bed027583da85e60e/",
"sizeInBytes": 182486
},
{
"link": "output",
"name": "versions.yml",
"path": "/89/082dfcf443ca9bed027583da85e60e/",
"sizeInBytes": 82
}
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"inputFilesBytes": 184264,
"outputFilesBytes": 182567,
"memoryInBytes": 3338240,
"writtenBytes": 182857,
"readBytes": 235430,
"runtimeInSeconds": 0.07
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.INDEX_MATURE",
"id": "9",
"type": "compute",
"command": {
"program": "bowtie-build mature.fa_igenome.fa_idx.fa fasta_bidx --threads 1\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE\":\n bowtie: $(echo $(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "mature.fa_igenome.fa_idx.fa",
"path": "/78/1eb176d18d15ba96f9cff9c1678bd7/",
"sizeInBytes": 99538
},
{
"link": "output",
"name": "fasta_bidx.1.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 4290349
},
{
"link": "output",
"name": "fasta_bidx.2.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 6988
},
{
"link": "output",
"name": "fasta_bidx.3.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 23300
},
{
"link": "output",
"name": "fasta_bidx.4.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 13968
},
{
"link": "output",
"name": "fasta_bidx.rev.1.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 4290349
},
{
"link": "output",
"name": "fasta_bidx.rev.2.ebwt",
"path": "/7e/378458c00515998d241fca889e702c/",
"sizeInBytes": 6988
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"link": "output",
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"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_SMRNASEQ.SMRNASEQ.MIRNA_QUANT.INDEX_HAIRPIN",
"id": "10",
"type": "compute",
"command": {
"program": "bowtie-build hairpin.fa_igenome.fa_idx.fa fasta_bidx --threads 1\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN\":\n bowtie: $(echo $(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "hairpin.fa_igenome.fa_idx.fa",
"path": "/89/082dfcf443ca9bed027583da85e60e/",
"sizeInBytes": 182486
},
{
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