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sarek-dirt02-001.json
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sarek-dirt02-001.json
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{
"name": "sarek",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-21T23:21:11.240833+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/sarek",
"runName": "marvelous_perlman",
"executedAt": "2023-03-21T13:21:06-10:00",
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},
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},
{
"name": "NFCORE_SAREK.SAREK.PREPARE_GENOME.BWAMEM1_INDEX",
"id": "6",
"type": "compute",
"command": {
"program": "mkdir bwa\n bwa \\\n index \\\n \\\n -p bwa/genome \\\n genome.fasta\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX\":\n bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//')\n END_VERSIONS",
"arguments": []
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{
"name": "NFCORE_SAREK.SAREK.PREPARE_GENOME.SAMTOOLS_FAIDX",
"id": "9",
"type": "compute",
"command": {
"program": "samtools \\\n faidx \\\n \\\n genome.fasta\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX\":\n samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')\n END_VERSIONS",
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},
{
"name": "NFCORE_SAREK.SAREK.PREPARE_GENOME.TABIX_KNOWN_INDELS",
"id": "2",
"type": "compute",
"command": {
"program": "tabix mills_and_1000G.indels.vcf.gz\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS\":\n tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
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},
{
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},
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"name": "NFCORE_SAREK.SAREK.PREPARE_INTERVALS.GATK4_INTERVALLISTTOBED",
"id": "7",
"type": "compute",
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}
],
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"runtimeInSeconds": 24.0
},
{
"name": "NFCORE_SAREK.SAREK.PREPARE_INTERVALS.CREATE_INTERVALS_BED",
"id": "5",
"type": "compute",
"command": {
"program": "grep -v '^@' genome.interval_list | awk -vFS=\"\t\" '{\n name = sprintf(\"%s_%d-%d\", $1, $2, $3);\n printf(\"%s\\t%d\\t%d\\n\", $1, $2-1, $3) > name \".bed\"\n }'\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED\":\n gawk: $(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')\n END_VERSIONS",
"arguments": []
},
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"files": [
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"link": "input",
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"link": "output",
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}
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"runtimeInSeconds": 0.0
},
{
"name": "NFCORE_SAREK.SAREK.PREPARE_GENOME.TABIX_DBSNP",
"id": "3",
"type": "compute",
"command": {
"program": "tabix dbsnp_146.hg38.vcf.gz\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP\":\n tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')\n END_VERSIONS",
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"runtimeInSeconds": 0.0
},
{
"name": "NFCORE_SAREK.SAREK.FASTQC",
"id": "12",
"type": "compute",
"command": {
"program": "printf \"%s\\n\" test_1.fastq.gz test_2.fastq.gz | while read f; do [[ $f =~ ^test-test_L1.* ]] || ln -s $f test-test_L1_$f ; done\n fastqc --quiet --threads 1 test-test_L1*\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK: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": "output",
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"link": "output",
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"runtimeInSeconds": 30.0
},
{
"name": "NFCORE_SAREK.SAREK.FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP.BWAMEM1_MEM",
"id": "14",
"type": "compute",
"command": {
"program": "INDEX=`find -L ./ -name \"*.amb\" | sed 's/.amb//'`\n\n bwa mem \\\n -K 100000000 -Y -R \"@RG\\tID:null.test.test_L1\\tPU:test_L1\\tSM:test_test\\tLB:test\\tDS:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta\\tPL:ILLUMINA\" \\\n -t 1 \\\n $INDEX \\\n test_1.fastq.gz test_2.fastq.gz \\\n | samtools sort --threads 1 -o test.sorted.bam -\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM\":\n bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//')\n samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')\n END_VERSIONS",
"arguments": []
},
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{
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"name": "test_1.fastq.gz",
"path": "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/",
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{
"link": "input",
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