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airrflow-dirt02-001.json
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{
"name": "airrflow",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-30T01:46:02.720872+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/airrflow",
"runName": "amazing_mercator",
"executedAt": "2023-03-29T15:45:52-10:00",
"tasks": [
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.FASTQ_INPUT_CHECK.SAMPLESHEET_CHECK",
"id": "3",
"type": "compute",
"command": {
"program": "check_samplesheet.py Metadata_test_airr.tsv\n cp Metadata_test_airr.tsv samplesheet.valid.tsv\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:FASTQ_INPUT_CHECK:SAMPLESHEET_CHECK\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n pandas: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('pandas').version)\"))\n END_VERSIONS",
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},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.VDJ_ANNOTATION.UNZIP_IMGT",
"id": "2",
"type": "compute",
"command": {
"program": "unzip imgtdb_base.zip\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:UNZIP_IMGT\":\n unzip: $(echo $(unzip -help 2>&1) | sed 's/^.*UnZip //; s/ of.*$//')\n END_VERSIONS",
"arguments": []
},
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},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.VDJ_ANNOTATION.UNZIP_IGBLAST",
"id": "1",
"type": "compute",
"command": {
"program": "unzip igblast_base.zip\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:VDJ_ANNOTATION:UNZIP_IGBLAST\":\n unzip: $(echo $(unzip -help 2>&1) | sed 's/^.*UnZip //; s/ of.*$//')\n END_VERSIONS",
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},
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{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "4",
"type": "compute",
"command": {
"program": "[ ! -f Sample1_1.fastq.gz ] && ln -sf Sample1_dn_R1.fastq.gz Sample1_1.fastq.gz\n [ ! -f Sample1_2.fastq.gz ] && ln -sf Sample1_dn_R2.fastq.gz Sample1_2.fastq.gz\n fastp \\\n --in1 Sample1_1.fastq.gz \\\n --in2 Sample1_2.fastq.gz \\\n --out1 Sample1_1.fastp.fastq.gz \\\n --out2 Sample1_2.fastp.fastq.gz \\\n --json Sample1.fastp.json \\\n --html Sample1.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample1.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
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},
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{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "5",
"type": "compute",
"command": {
"program": "[ ! -f Sample2_1.fastq.gz ] && ln -sf Sample2_m_R1.fastq.gz Sample2_1.fastq.gz\n [ ! -f Sample2_2.fastq.gz ] && ln -sf Sample2_m_R2.fastq.gz Sample2_2.fastq.gz\n fastp \\\n --in1 Sample2_1.fastq.gz \\\n --in2 Sample2_2.fastq.gz \\\n --out1 Sample2_1.fastp.fastq.gz \\\n --out2 Sample2_2.fastp.fastq.gz \\\n --json Sample2.fastp.json \\\n --html Sample2.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample2.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
},
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},
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "6",
"type": "compute",
"command": {
"program": "[ ! -f Sample3_1.fastq.gz ] && ln -sf Sample3_n_R1.fastq.gz Sample3_1.fastq.gz\n [ ! -f Sample3_2.fastq.gz ] && ln -sf Sample3_n_R2.fastq.gz Sample3_2.fastq.gz\n fastp \\\n --in1 Sample3_1.fastq.gz \\\n --in2 Sample3_2.fastq.gz \\\n --out1 Sample3_1.fastp.fastq.gz \\\n --out2 Sample3_2.fastp.fastq.gz \\\n --json Sample3.fastp.json \\\n --html Sample3.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample3.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
},
"parents": [],
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},
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"program": "[ ! -f Sample4_1.fastq.gz ] && ln -sf Sample4_p_R1.fastq.gz Sample4_1.fastq.gz\n [ ! -f Sample4_2.fastq.gz ] && ln -sf Sample4_p_R2.fastq.gz Sample4_2.fastq.gz\n fastp \\\n --in1 Sample4_1.fastq.gz \\\n --in2 Sample4_2.fastq.gz \\\n --out1 Sample4_1.fastp.fastq.gz \\\n --out2 Sample4_2.fastp.fastq.gz \\\n --json Sample4.fastp.json \\\n --html Sample4.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample4.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
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"parents": [],
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"link": "input",
"name": "Sample4_p_R1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 302843
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"link": "input",
"name": "Sample4_p_R2.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
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"link": "output",
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"link": "output",
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"link": "output",
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"sizeInBytes": 155334
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"link": "output",
"name": "Sample4.fastp.html",
"path": "/76/6e9f9e0b2d8c845c4bafe8dce64978/",
"sizeInBytes": 524774
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"link": "output",
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"link": "output",
"name": "versions.yml",
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "8",
"type": "compute",
"command": {
"program": "[ ! -f Sample5_1.fastq.gz ] && ln -sf Sample5_dn_R1.fastq.gz Sample5_1.fastq.gz\n [ ! -f Sample5_2.fastq.gz ] && ln -sf Sample5_dn_R2.fastq.gz Sample5_2.fastq.gz\n fastp \\\n --in1 Sample5_1.fastq.gz \\\n --in2 Sample5_2.fastq.gz \\\n --out1 Sample5_1.fastp.fastq.gz \\\n --out2 Sample5_2.fastp.fastq.gz \\\n --json Sample5.fastp.json \\\n --html Sample5.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample5.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
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"parents": [],
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"link": "input",
"name": "Sample5_dn_R1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 353422
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"link": "input",
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"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
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"link": "output",
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"link": "output",
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"sizeInBytes": 422821
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"link": "output",
"name": "Sample5.fastp.json",
"path": "/2b/3afc9dc5b0c6d9c3c60f64c35557a0/",
"sizeInBytes": 148750
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"link": "output",
"name": "Sample5.fastp.html",
"path": "/2b/3afc9dc5b0c6d9c3c60f64c35557a0/",
"sizeInBytes": 518644
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"link": "output",
"name": "Sample5.fastp.log",
"path": "/2b/3afc9dc5b0c6d9c3c60f64c35557a0/",
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"link": "output",
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "9",
"type": "compute",
"command": {
"program": "[ ! -f Sample6_1.fastq.gz ] && ln -sf Sample6_p_R1.fastq.gz Sample6_1.fastq.gz\n [ ! -f Sample6_2.fastq.gz ] && ln -sf Sample6_p_R2.fastq.gz Sample6_2.fastq.gz\n fastp \\\n --in1 Sample6_1.fastq.gz \\\n --in2 Sample6_2.fastq.gz \\\n --out1 Sample6_1.fastp.fastq.gz \\\n --out2 Sample6_2.fastp.fastq.gz \\\n --json Sample6.fastp.json \\\n --html Sample6.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample6.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
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"parents": [],
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"files": [
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"link": "input",
"name": "Sample6_p_R1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 307768
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"link": "input",
"name": "Sample6_p_R2.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 358144
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"link": "output",
"name": "Sample6_1.fastp.fastq.gz",
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"link": "output",
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"sizeInBytes": 386775
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"link": "output",
"name": "Sample6.fastp.json",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
"sizeInBytes": 150357
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"link": "output",
"name": "Sample6.fastp.html",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
"sizeInBytes": 520235
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"link": "output",
"name": "Sample6.fastp.log",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
"sizeInBytes": 1241
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"link": "output",
"name": "versions.yml",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "10",
"type": "compute",
"command": {
"program": "[ ! -f Sample7_1.fastq.gz ] && ln -sf Sample7_n_R1.fastq.gz Sample7_1.fastq.gz\n [ ! -f Sample7_2.fastq.gz ] && ln -sf Sample7_n_R2.fastq.gz Sample7_2.fastq.gz\n fastp \\\n --in1 Sample7_1.fastq.gz \\\n --in2 Sample7_2.fastq.gz \\\n --out1 Sample7_1.fastp.fastq.gz \\\n --out2 Sample7_2.fastp.fastq.gz \\\n --json Sample7.fastp.json \\\n --html Sample7.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample7.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
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"link": "input",
"name": "Sample7_n_R1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 334625
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"link": "input",
"name": "Sample7_n_R2.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 379714
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"link": "output",
"name": "Sample7_1.fastp.fastq.gz",
"path": "/a5/e5be4ba7e03b80f498252a0a1885de/",
"sizeInBytes": 359192
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"link": "output",
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"sizeInBytes": 410519
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"link": "output",
"name": "Sample7.fastp.json",
"path": "/a5/e5be4ba7e03b80f498252a0a1885de/",
"sizeInBytes": 150717
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"link": "output",
"name": "Sample7.fastp.html",
"path": "/a5/e5be4ba7e03b80f498252a0a1885de/",
"sizeInBytes": 520311
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"link": "output",
"name": "Sample7.fastp.log",
"path": "/a5/e5be4ba7e03b80f498252a0a1885de/",
"sizeInBytes": 1241
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"link": "output",
"name": "versions.yml",
"path": "/a5/e5be4ba7e03b80f498252a0a1885de/",
"sizeInBytes": 81
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"runtimeInSeconds": 1.0
},
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.FASTP",
"id": "11",
"type": "compute",
"command": {
"program": "[ ! -f Sample8_1.fastq.gz ] && ln -sf Sample8_m_R1.fastq.gz Sample8_1.fastq.gz\n [ ! -f Sample8_2.fastq.gz ] && ln -sf Sample8_m_R2.fastq.gz Sample8_2.fastq.gz\n fastp \\\n --in1 Sample8_1.fastq.gz \\\n --in2 Sample8_2.fastq.gz \\\n --out1 Sample8_1.fastp.fastq.gz \\\n --out2 Sample8_2.fastp.fastq.gz \\\n --json Sample8.fastp.json \\\n --html Sample8.fastp.html \\\n \\\n \\\n \\\n --thread 1 \\\n --detect_adapter_for_pe \\\n --disable_quality_filtering --disable_length_filtering true \\\n 2> Sample8.fastp.log\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:FASTP\":\n fastp: $(fastp --version 2>&1 | sed -e \"s/fastp //g\")\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample8_m_R1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 363568
},
{
"link": "input",
"name": "Sample8_m_R2.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 399964
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{
"link": "output",
"name": "Sample8_1.fastp.fastq.gz",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
"sizeInBytes": 387900
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{
"link": "output",
"name": "Sample8_2.fastp.fastq.gz",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
"sizeInBytes": 430333
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{
"link": "output",
"name": "Sample8.fastp.json",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
"sizeInBytes": 148070
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{
"link": "output",
"name": "Sample8.fastp.html",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
"sizeInBytes": 518035
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{
"link": "output",
"name": "Sample8.fastp.log",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
"sizeInBytes": 1244
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"link": "output",
"name": "versions.yml",
"path": "/de/c784f6972f50b6fa7033a8cc870f2f/",
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"runtimeInSeconds": 1.0
},
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "12",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample1_1.fastp.fastq.gz\" -I1 \"Sample1_dn_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample1_UMI_R1.fastq.gz\"\n mv \"Sample1_2.fastp.fastq.gz\" \"Sample1_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample1_1.fastp.fastq.gz",
"path": "/98/86663c339c4ae52eb37a27a4055fb2/",
"sizeInBytes": 434376
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{
"link": "input",
"name": "Sample1_2.fastp.fastq.gz",
"path": "/98/86663c339c4ae52eb37a27a4055fb2/",
"sizeInBytes": 483936
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{
"link": "input",
"name": "Sample1_dn_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 38297
},
{
"link": "output",
"name": "Sample1_UMI_R1.fastq.gz",
"path": "/96/a57ebc5104523c2bfe5f5af66213d6/",
"sizeInBytes": 412017
},
{
"link": "output",
"name": "Sample1_R2.fastq.gz",
"path": "/96/a57ebc5104523c2bfe5f5af66213d6/",
"sizeInBytes": 483936
},
{
"link": "output",
"name": "versions.yml",
"path": "/96/a57ebc5104523c2bfe5f5af66213d6/",
"sizeInBytes": 105
}
],
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"runtimeInSeconds": 2.0
},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "13",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample2_1.fastp.fastq.gz\" -I1 \"Sample2_m_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample2_UMI_R1.fastq.gz\"\n mv \"Sample2_2.fastp.fastq.gz\" \"Sample2_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample2_1.fastp.fastq.gz",
"path": "/c4/4d7efaaa83c87f700efb7c3d370e69/",
"sizeInBytes": 433951
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{
"link": "input",
"name": "Sample2_2.fastp.fastq.gz",
"path": "/c4/4d7efaaa83c87f700efb7c3d370e69/",
"sizeInBytes": 477794
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{
"link": "input",
"name": "Sample2_m_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 37762
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{
"link": "output",
"name": "Sample2_UMI_R1.fastq.gz",
"path": "/4a/4a083de57cdf10403c3f8d0bf893c4/",
"sizeInBytes": 411537
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{
"link": "output",
"name": "Sample2_R2.fastq.gz",
"path": "/4a/4a083de57cdf10403c3f8d0bf893c4/",
"sizeInBytes": 477794
},
{
"link": "output",
"name": "versions.yml",
"path": "/4a/4a083de57cdf10403c3f8d0bf893c4/",
"sizeInBytes": 105
}
],
"avgCPU": 93.7,
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"runtimeInSeconds": 2.0
},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "14",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample3_1.fastp.fastq.gz\" -I1 \"Sample3_n_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample3_UMI_R1.fastq.gz\"\n mv \"Sample3_2.fastp.fastq.gz\" \"Sample3_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
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"files": [
{
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"name": "Sample3_1.fastp.fastq.gz",
"path": "/4d/8c39c8e913caa495ab100f4f77ed49/",
"sizeInBytes": 407467
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{
"link": "input",
"name": "Sample3_2.fastp.fastq.gz",
"path": "/4d/8c39c8e913caa495ab100f4f77ed49/",
"sizeInBytes": 473955
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{
"link": "input",
"name": "Sample3_n_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 38434
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{
"link": "output",
"name": "Sample3_UMI_R1.fastq.gz",
"path": "/aa/0e67de11aa6cf0080bbc866f93dcc5/",
"sizeInBytes": 390072
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{
"link": "output",
"name": "Sample3_R2.fastq.gz",
"path": "/aa/0e67de11aa6cf0080bbc866f93dcc5/",
"sizeInBytes": 473955
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{
"link": "output",
"name": "versions.yml",
"path": "/aa/0e67de11aa6cf0080bbc866f93dcc5/",
"sizeInBytes": 105
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"runtimeInSeconds": 2.0
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"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "15",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample4_1.fastp.fastq.gz\" -I1 \"Sample4_p_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample4_UMI_R1.fastq.gz\"\n mv \"Sample4_2.fastp.fastq.gz\" \"Sample4_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample4_1.fastp.fastq.gz",
"path": "/76/6e9f9e0b2d8c845c4bafe8dce64978/",
"sizeInBytes": 324464
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{
"link": "input",
"name": "Sample4_2.fastp.fastq.gz",
"path": "/76/6e9f9e0b2d8c845c4bafe8dce64978/",
"sizeInBytes": 382350
},
{
"link": "input",
"name": "Sample4_p_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 42006
},
{
"link": "output",
"name": "Sample4_UMI_R1.fastq.gz",
"path": "/a3/b528232e9ab0984927e2c59c640106/",
"sizeInBytes": 307450
},
{
"link": "output",
"name": "Sample4_R2.fastq.gz",
"path": "/a3/b528232e9ab0984927e2c59c640106/",
"sizeInBytes": 382350
},
{
"link": "output",
"name": "versions.yml",
"path": "/a3/b528232e9ab0984927e2c59c640106/",
"sizeInBytes": 105
}
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"writtenBytes": 307898,
"readBytes": 4822856,
"runtimeInSeconds": 2.0
},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "16",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample5_1.fastp.fastq.gz\" -I1 \"Sample5_dn_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample5_UMI_R1.fastq.gz\"\n mv \"Sample5_2.fastp.fastq.gz\" \"Sample5_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample5_1.fastp.fastq.gz",
"path": "/2b/3afc9dc5b0c6d9c3c60f64c35557a0/",
"sizeInBytes": 378141
},
{
"link": "input",
"name": "Sample5_2.fastp.fastq.gz",
"path": "/2b/3afc9dc5b0c6d9c3c60f64c35557a0/",
"sizeInBytes": 422821
},
{
"link": "input",
"name": "Sample5_dn_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 34786
},
{
"link": "output",
"name": "Sample5_UMI_R1.fastq.gz",
"path": "/ff/64442b8ec02922ff6ecf0e0e7afa1d/",
"sizeInBytes": 353888
},
{
"link": "output",
"name": "Sample5_R2.fastq.gz",
"path": "/ff/64442b8ec02922ff6ecf0e0e7afa1d/",
"sizeInBytes": 422821
},
{
"link": "output",
"name": "versions.yml",
"path": "/ff/64442b8ec02922ff6ecf0e0e7afa1d/",
"sizeInBytes": 105
}
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},
{
"name": "NFCORE_AIRRFLOW.AIRRFLOW.SEQUENCE_ASSEMBLY.PRESTO_UMI.MERGE_UMI",
"id": "17",
"type": "compute",
"command": {
"program": "merge_R1_umi.py -R1 \"Sample6_1.fastp.fastq.gz\" -I1 \"Sample6_p_I1.fastq.gz\" -o UMI_R1.fastq.gz --umi_start 6 --umi_length 8\n mv \"UMI_R1.fastq.gz\" \"Sample6_UMI_R1.fastq.gz\"\n mv \"Sample6_2.fastp.fastq.gz\" \"Sample6_R2.fastq.gz\"\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_AIRRFLOW:AIRRFLOW:SEQUENCE_ASSEMBLY:PRESTO_UMI:MERGE_UMI\":\n python: $( echo $(python --version | grep -o \"[0-9\\. ]\\+\") )\n biopython: $(echo $(python -c \"import pkg_resources; print(pkg_resources.get_distribution('biopython').version)\"))\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "Sample6_1.fastp.fastq.gz",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
"sizeInBytes": 332619
},
{
"link": "input",
"name": "Sample6_2.fastp.fastq.gz",
"path": "/b8/206b6d08ea350ffdf9c3b6d1afffae/",
"sizeInBytes": 386775
},
{
"link": "input",
"name": "Sample6_p_I1.fastq.gz",
"path": "/nf-core/test-datasets/airrflow/testdata-bcr/",
"sizeInBytes": 35669
},
{
"link": "output",
"name": "Sample6_UMI_R1.fastq.gz",
"path": "/84/f1770dbefa38688f096ea3f5491cd2/",
"sizeInBytes": 309973
},
{
"link": "output",
"name": "Sample6_R2.fastq.gz",
"path": "/84/f1770dbefa38688f096ea3f5491cd2/",
"sizeInBytes": 386775
},
{
"link": "output",
"name": "versions.yml",
"path": "/84/f1770dbefa38688f096ea3f5491cd2/",
"sizeInBytes": 105
}