.gitignore

@@ -0,0 +1 @@
+.nextflow*

.treeDag.json

@@ -1 +1 @@
-{"name": "root", "children": [{"name": "integrity_coverage_1_1", "process": {"pid": "1_1", "input": "fastq", "output": "fastq", "lane": 1, "directives": "integrity_coverage"}, "children": [{"name": "fastqc_trimmomatic_1_2", "process": {"pid": "1_2", "input": "fastq", "output": "fastq", "lane": 1, "directives": "fastqccpus: 2memory: 4GBcontainer: flowcraft/fastqcversion: 0.11.7-1trimmomaticcpus: 2memory: { 4.GB * task.attempt }container: flowcraft/trimmomaticversion: 0.36-1"}, "children": [{"name": "filter_poly_1_3", "process": {"pid": "1_3", "input": "fastq", "output": "fastq", "lane": 1, "directives": "filter_polycpus: 1memory: { 4.GB * task.attempt }container: flowcraft/prinseqversion: 0.20.4-1"}, "children": [{"name": "bowtie_1_4", "process": {"pid": "1_4", "input": "fastq", "output": "bam", "lane": 1, "directives": "bowtiecontainer: flowcraft/bowtie_dengueversion: 2-1memory: {5.Gb*task.attempt}cpus: 4bowtie_buildcontainer: flowcraft/bowtie_dengueversion: 2-1memory: {5.Gb*task.attempt}cpus: 1"}, "children": [{"name": "retrieve_mapped_1_5", "process": {"pid": "1_5", "input": "bam", "output": "fastq", "lane": 1, "directives": "retrieve_mappedcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 2"}, "children": [{"name": "viral_assembly_1_6", "process": {"pid": "1_6", "input": "fastq", "output": "fasta", "lane": 1, "directives": "va_spadescpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: trueva_megahitcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: true"}, "children": [{"name": "assembly_mapping_1_7", "process": {"pid": "1_7", "input": "fasta", "output": "fasta", "lane": 1, "directives": "assembly_mappingcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1process_assembly_mappingcpus: 1memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1"}, "children": [{"name": "pilon_1_8", "process": {"pid": "1_8", "input": "fasta", "output": "fasta", "lane": 1, "directives": "piloncpus: 4memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1pilon_reportcpus: 1memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1"}, "children": [{"name": "split_assembly_1_9", "process": {"pid": "1_9", "input": "fasta", "output": "fasta", "lane": 1, "directives": "split_assemblycpus: 1memory: { 1.GB * task.attempt }"}, "children": [{"name": "dengue_typing_1_10", "process": {"pid": "1_10", "input": "fasta", "output": "fasta", "lane": 1, "directives": "dengue_typingcpus: 4memory: 4GBcontainer: flowcraft/seq_typingversion: 2.0-1"}, "children": [{"name": "mafft_1_11", "process": {"pid": "1_11", "input": "fasta", "output": "align", "lane": 1, "directives": "mafftcontainer: flowcraft/mafftversion: 7.402-1cpus: 4memory: { 4.GB * task.attempt }"}, "children": [{"name": "raxml_1_12", "process": {"pid": "1_12", "input": "align", "output": ".tree", "lane": 1, "directives": "raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2cpus: 4memory: { 4.GB * task.attempt }report_raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2"}, "children": []}]}]}]}]}]}]}]}]}]}]}]}]}
+{"name": "root", "children": [{"name": "integrity_coverage_1_1", "process": {"pid": "1_1", "input": "fastq", "output": "fastq", "lane": 1, "directives": "integrity_coverage"}, "children": [{"name": "fastqc_trimmomatic_1_2", "process": {"pid": "1_2", "input": "fastq", "output": "fastq", "lane": 1, "directives": "fastqccpus: 2memory: 4GBcontainer: flowcraft/fastqcversion: 0.11.7-1trimmomaticcpus: 2memory: { 4.GB * task.attempt }container: flowcraft/trimmomaticversion: 0.36-1"}, "children": [{"name": "filter_poly_1_3", "process": {"pid": "1_3", "input": "fastq", "output": "fastq", "lane": 1, "directives": "filter_polycpus: 1memory: { 4.GB * task.attempt }container: flowcraft/prinseqversion: 0.20.4-1"}, "children": [{"name": "bowtie_1_4", "process": {"pid": "1_4", "input": "fastq", "output": "bam", "lane": 1, "directives": "bowtiecontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 4bowtie_buildcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 1"}, "children": [{"name": "retrieve_mapped_1_5", "process": {"pid": "1_5", "input": "bam", "output": "fastq", "lane": 1, "directives": "retrieve_mappedcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 2"}, "children": [{"name": "check_coverage_1_6", "process": {"pid": "1_6", "input": "fastq", "output": "fastq", "lane": 1, "directives": "check_coverage"}, "children": [{"name": "viral_assembly_1_7", "process": {"pid": "1_7", "input": "fastq", "output": "fasta", "lane": 1, "directives": "va_spadescpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: trueva_megahitcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: true"}, "children": [{"name": "assembly_mapping_1_8", "process": {"pid": "1_8", "input": "fasta", "output": "fasta", "lane": 1, "directives": "assembly_mappingcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1process_assembly_mappingcpus: 1memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1"}, "children": [{"name": "pilon_1_9", "process": {"pid": "1_9", "input": "fasta", "output": "fasta", "lane": 1, "directives": "piloncpus: 4memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1pilon_reportcpus: 1memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1"}, "children": [{"name": "split_assembly_1_10", "process": {"pid": "1_10", "input": "fasta", "output": "fasta", "lane": 1, "directives": "split_assemblycpus: 1memory: { 1.GB * task.attempt }"}, "children": [{"name": "dengue_typing_1_11", "process": {"pid": "1_11", "input": "fasta", "output": "fasta", "lane": 1, "directives": "dengue_typing_assemblycpus: 4memory: 1GBcontainer: flowcraft/seq_typingversion: 2.0-1dengue_typing_readscpus: 4memory: { 5.GB * task.attempt }container: ummidock/seq_typingversion: 2.2-02"}, "children": [{"name": "mafft_1_12", "process": {"pid": "1_12", "input": "fasta", "output": "align", "lane": 1, "directives": "mafftcontainer: flowcraft/mafftversion: 7.402-1cpus: 4memory: { 4.GB * task.attempt }"}, "children": [{"name": "raxml_1_13", "process": {"pid": "1_13", "input": "align", "output": ".tree", "lane": 1, "directives": "raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2cpus: 4memory: { 4.GB * task.attempt }report_raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2"}, "children": []}]}]}]}]}]}]}]}]}]}]}]}]}]}

DEN-IM.html

@@ -34,7 +34,7 @@
 <script src="https://d3js.org/d3.v4.min.js"></script>
 <script>
     // fetchs data using jinja
-    const inputData = {'name': 'root', 'children': [{'name': 'integrity_coverage_1_1', 'process': {'pid': '1_1', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'integrity_coverage'}, 'children': [{'name': 'fastqc_trimmomatic_1_2', 'process': {'pid': '1_2', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'fastqccpus: 2memory: 4GBcontainer: flowcraft/fastqcversion: 0.11.7-1trimmomaticcpus: 2memory: { 4.GB * task.attempt }container: flowcraft/trimmomaticversion: 0.36-1'}, 'children': [{'name': 'filter_poly_1_3', 'process': {'pid': '1_3', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'filter_polycpus: 1memory: { 4.GB * task.attempt }container: flowcraft/prinseqversion: 0.20.4-1'}, 'children': [{'name': 'bowtie_1_4', 'process': {'pid': '1_4', 'input': 'fastq', 'output': 'bam', 'lane': 1, 'directives': 'bowtiecontainer: flowcraft/bowtie_dengueversion: 2-1memory: {5.Gb*task.attempt}cpus: 4bowtie_buildcontainer: flowcraft/bowtie_dengueversion: 2-1memory: {5.Gb*task.attempt}cpus: 1'}, 'children': [{'name': 'retrieve_mapped_1_5', 'process': {'pid': '1_5', 'input': 'bam', 'output': 'fastq', 'lane': 1, 'directives': 'retrieve_mappedcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 2'}, 'children': [{'name': 'viral_assembly_1_6', 'process': {'pid': '1_6', 'input': 'fastq', 'output': 'fasta', 'lane': 1, 'directives': 'va_spadescpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: trueva_megahitcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: true'}, 'children': [{'name': 'assembly_mapping_1_7', 'process': {'pid': '1_7', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'assembly_mappingcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1process_assembly_mappingcpus: 1memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1'}, 'children': [{'name': 'pilon_1_8', 'process': {'pid': '1_8', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'piloncpus: 4memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1pilon_reportcpus: 1memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1'}, 'children': [{'name': 'split_assembly_1_9', 'process': {'pid': '1_9', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'split_assemblycpus: 1memory: { 1.GB * task.attempt }'}, 'children': [{'name': 'dengue_typing_1_10', 'process': {'pid': '1_10', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'dengue_typingcpus: 4memory: 4GBcontainer: flowcraft/seq_typingversion: 2.0-1'}, 'children': [{'name': 'mafft_1_11', 'process': {'pid': '1_11', 'input': 'fasta', 'output': 'align', 'lane': 1, 'directives': 'mafftcontainer: flowcraft/mafftversion: 7.402-1cpus: 4memory: { 4.GB * task.attempt }'}, 'children': [{'name': 'raxml_1_12', 'process': {'pid': '1_12', 'input': 'align', 'output': '.tree', 'lane': 1, 'directives': 'raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2cpus: 4memory: { 4.GB * task.attempt }report_raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2'}, 'children': []}]}]}]}]}]}]}]}]}]}]}]}]}
+    const inputData = {'name': 'root', 'children': [{'name': 'integrity_coverage_1_1', 'process': {'pid': '1_1', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'integrity_coverage'}, 'children': [{'name': 'fastqc_trimmomatic_1_2', 'process': {'pid': '1_2', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'fastqccpus: 2memory: 4GBcontainer: flowcraft/fastqcversion: 0.11.7-1trimmomaticcpus: 2memory: { 4.GB * task.attempt }container: flowcraft/trimmomaticversion: 0.36-1'}, 'children': [{'name': 'filter_poly_1_3', 'process': {'pid': '1_3', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'filter_polycpus: 1memory: { 4.GB * task.attempt }container: flowcraft/prinseqversion: 0.20.4-1'}, 'children': [{'name': 'bowtie_1_4', 'process': {'pid': '1_4', 'input': 'fastq', 'output': 'bam', 'lane': 1, 'directives': 'bowtiecontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 4bowtie_buildcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 1'}, 'children': [{'name': 'retrieve_mapped_1_5', 'process': {'pid': '1_5', 'input': 'bam', 'output': 'fastq', 'lane': 1, 'directives': 'retrieve_mappedcontainer: flowcraft/bowtie2_samtoolsversion: 1.0.0-1memory: {5.Gb*task.attempt}cpus: 2'}, 'children': [{'name': 'check_coverage_1_6', 'process': {'pid': '1_6', 'input': 'fastq', 'output': 'fastq', 'lane': 1, 'directives': 'check_coverage'}, 'children': [{'name': 'viral_assembly_1_7', 'process': {'pid': '1_7', 'input': 'fastq', 'output': 'fasta', 'lane': 1, 'directives': 'va_spadescpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: trueva_megahitcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/viral_assemblyversion: 0.1-1scratch: true'}, 'children': [{'name': 'assembly_mapping_1_8', 'process': {'pid': '1_8', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'assembly_mappingcpus: 4memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1process_assembly_mappingcpus: 1memory: { 5.GB * task.attempt }container: flowcraft/bowtie2_samtoolsversion: 1.0.0-1'}, 'children': [{'name': 'pilon_1_9', 'process': {'pid': '1_9', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'piloncpus: 4memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1pilon_reportcpus: 1memory: { 7.GB * task.attempt }container: flowcraft/pilonversion: 1.22.0-1'}, 'children': [{'name': 'split_assembly_1_10', 'process': {'pid': '1_10', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'split_assemblycpus: 1memory: { 1.GB * task.attempt }'}, 'children': [{'name': 'dengue_typing_1_11', 'process': {'pid': '1_11', 'input': 'fasta', 'output': 'fasta', 'lane': 1, 'directives': 'dengue_typing_assemblycpus: 4memory: 1GBcontainer: flowcraft/seq_typingversion: 2.0-1dengue_typing_readscpus: 4memory: { 5.GB * task.attempt }container: ummidock/seq_typingversion: 2.2-02'}, 'children': [{'name': 'mafft_1_12', 'process': {'pid': '1_12', 'input': 'fasta', 'output': 'align', 'lane': 1, 'directives': 'mafftcontainer: flowcraft/mafftversion: 7.402-1cpus: 4memory: { 4.GB * task.attempt }'}, 'children': [{'name': 'raxml_1_13', 'process': {'pid': '1_13', 'input': 'align', 'output': '.tree', 'lane': 1, 'directives': 'raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2cpus: 4memory: { 4.GB * task.attempt }report_raxmlcontainer: flowcraft/raxmlversion: 8.2.11-2'}, 'children': []}]}]}]}]}]}]}]}]}]}]}]}]}]}
 
     /**
      * This function creates a tooltip with the node/process information