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output_definition.json
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{
"rna.align": {
"anno_flagstat": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/transcriptome flagstats",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Anno.\\nFlagstat\\nQC\"]",
"subgraph": "cluster_rep${i+1}"
},
"anno_flagstat_json": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/transcriptome flagstats json"
},
"annobam": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/transcriptome alignments",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Anno.\\nBAM\"]",
"subgraph": "cluster_rep${i+1}"
},
"genome_flagstat": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/genome flagstats",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Genome.\\nFlagstat\\nQC\"]",
"subgraph": "cluster_rep${i+1}"
},
"genome_flagstat_json": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/genome flagstats json"
},
"genomebam": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/genome alignments",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Genome\\nBAM\"]",
"subgraph": "cluster_rep${i+1}"
},
"log": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/STAR log"
},
"log_json": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/STAR log json"
},
"python_log": {
"path": "align/rep${i+1}/${basename}",
"table": "Align/Replicate ${i+1}/python log"
}
},
"rna.bam_to_signals": {
"all_minus": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from minus strand",
"ucsc_track": "track type=bigWig name=\"rep${i+1} all minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"All -\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
},
"all_plus": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads from plus strand",
"ucsc_track": "track type=bigWig name=\"rep${i+1} all plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"All +\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
},
"all_unstranded": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of all reads",
"ucsc_track": "track type=bigWig name=\"rep${i+1} all\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"All .\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
},
"python_log": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/python log"
},
"unique_minus": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from minus strand",
"ucsc_track": "track type=bigWig name=\"rep${i+1} unique minus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off negateValues=on viewLimits=-1:0 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Uniq -\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
},
"unique_plus": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads from plus strand",
"ucsc_track": "track type=bigWig name=\"rep${i+1} unique plus\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Uniq +\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
},
"unique_unstranded": {
"path": "bam_to_signals/rep${i+1}/${basename}",
"table": "Bam_to_signals/Replicate ${i+1}/signal track of unique reads",
"ucsc_track": "track type=bigWig name=\"rep${i+1} unique\" priority=${i+1} visibility=full smoothingWindow=off windowingFunction=mean+whiskers autoScale=off viewLimits=0:1 transformFunc=LOG maxHeightPixels=64:18:8",
"node": "[shape=box style=\"filled, rounded\" fillcolor=lightyellow label=\"Uniq .\\nsignal\"]",
"subgraph": "cluster_rep${i+1}"
}
},
"rna.kallisto": {
"python_log": {
"path": "kallisto/rep${i+1}/${basename}",
"table": "Kallisto/Replicate ${i+1}/python log"
},
"quants": {
"path": "kallisto/rep${i+1}/${basename}",
"table": "Kallisto/Replicate ${i+1}/kallisto quants",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Kallisto\\nQuants\"]",
"subgraph": "cluster_rep${i+1}"
}
},
"rna.mad_qc": {
"madQCmetrics": {
"path": "mad_qc/${basename}",
"table": "Mad_QC/Mad QC metrics json"
},
"madQCplot": {
"path": "mad_qc/${basename}",
"table": "Mad_QC/Mad QC plot",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Mad QC\\nPlot\"]",
"subgraph": "cluster_rep${i+1}"
},
"python_log": {
"path": "mad_qc/${basename}",
"table": "Mad_QC/python log"
}
},
"rna.rna_qc": {
"python_log": {
"path": "rna_qc/rep${i+1}/${basename}",
"table": "RNA_QC/Replicate ${i+1}/python log"
},
"rnaQC": {
"path": "rna_qc/rep${i+1}/${basename}",
"table": "RNA_QC/Replicate ${i+1}/rna qc metrics json",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"RNA\\nQC\"]",
"subgraph": "cluster_rep${i+1}"
}
},
"rna.rsem_quant": {
"genes_results": {
"path": "rsem_quant/rep${i+1}/${basename}",
"table": "Rsem_quant/Replicate ${i+1}/gene quants",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Genes\\nQuants\"]",
"subgraph": "cluster_rep${i+1}"
},
"isoforms_results": {
"path": "rsem_quant/rep${i+1}/${basename}",
"table": "Rsem_quant/Replicate ${i+1}/isoform quants",
"node": "[shape=oval style=\"filled\" fillcolor=gainsboro fontsize=6 margin=0 label=\"Isoforms\\nQuants\"]",
"subgraph": "cluster_rep${i+1}"
},
"number_of_genes": {
"path": "rsem_quant/rep${i+1}/${basename}",
"table": "Rsem_quant/Replicate ${i+1}/number of genes detected json"
},
"python_log": {
"path": "rsem_quant/rep${i+1}/${basename}",
"table": "Rsem_quant/Replicate ${i+1}/python log"
}
},
"inputs": {
"rna.fastqs_R1": {
"node": "[shape=box style=\"filled, rounded\" fillcolor=pink label=\"FASTQ\\nR1 (${i+1},${j+1})\"]",
"subgraph": "cluster_rep${i+1}"
},
"rna.fastqs_R2": {
"node": "[shape=box style=\"filled, rounded\" fillcolor=pink label=\"FASTQ\\nR2 (${i+1},${j+1})\"]",
"subgraph": "cluster_rep${i+1}"
},
"rna.align_index": {
"node": "[shape=box style=\"filled, rounded\" fillcolor=pink label=\"STAR\\nIndex\"]"
},
"rna.kallisto_index": {
"node": "[shape=box style=\"filled, rounded\" fillcolor=pink label=\"Kallisto\\nIndex\"]"
},
"rna.rsem_index": {
"node": "[shape=box style=\"filled, rounded\" fillcolor=pink label=\"RSEM\\nIndex\"]"
}
},
"task_graph_template": {
"graph [rankdir=LR nodesep=0.1 ranksep=0.3]": null,
"node [shape=box fontsize=9 margin=0.05 penwidth=0.5 height=0 fillcolor=lightcyan color=grey style=filled]": null,
"edge [arrowsize=0.5 color=grey penwidth=0.5]": null,
"subgraph cluster_rep1": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 1\""},
"subgraph cluster_rep2": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 2\""},
"subgraph cluster_rep3": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 3\""},
"subgraph cluster_rep4": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 4\""},
"subgraph cluster_rep5": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 5\""},
"subgraph cluster_rep6": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 6\""},
"subgraph cluster_rep7": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 7\""},
"subgraph cluster_rep8": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 8\""},
"subgraph cluster_rep9": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 9\""},
"subgraph cluster_rep10": {"style": "\"filled, dashed\"", "fontsize": "9", "color": "grey", "penwidth": "0.5", "fillcolor": "honeydew", "labeljust": "\"l\"", "label": "\"Replicate 10\""}
}
}