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Implemented circos flag for purple #260

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Implemented circos flag for purple #260

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4 changes: 3 additions & 1 deletion modules/local/purple/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,8 @@ process PURPLE {
def target_region_ratios_arg = target_region_ratios ? "-target_regions_ratios ${target_region_ratios}" : ''
def target_region_msi_indels_arg = target_region_msi_indels ? "-target_regions_msi_indels ${target_region_msi_indels}" : ''

def purple_circos_arg = params.purple_circos ? "-circos \$(which circos)" : ''

"""
purple \\
-Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
Expand All @@ -76,7 +78,7 @@ process PURPLE {
${target_region_msi_indels_arg} \\
${germline_del_arg} \\
-gc_profile ${gc_profile} \\
-circos \$(which circos) \\
${purple_circos_arg} \\
-threads ${task.cpus} \\
${log_level_arg} \\
-output_dir purple/
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2 changes: 2 additions & 0 deletions nextflow.config
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Expand Up @@ -46,6 +46,8 @@ params {
isofox_read_length = null
isofox_functions = 'TRANSCRIPT_COUNTS;ALT_SPLICE_JUNCTIONS;FUSIONS;RETAINED_INTRONS'

purple_circos = true

// NOTE(SW): used only for panel resource creation
driver_gene_panel = null
target_regions_bed = null
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6 changes: 6 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -191,6 +191,12 @@
"description": "Log level filter for WiGiTS modules",
"default": "DEBUG",
"fa_icon": "fas fa-cog"
},
"purple_circos": {
"type": "boolean",
"description": "Enable Circos plot generation for purple.",
"default": true,
"fa_icon": "fas fa-cog"
}
}
},
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