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comparison CSP2/subworkflows/fetchData/main.nf @ 28:893a6993efe3

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 13:48:13 -0500
parents 792274118b2e
children b6ec322b1f05
comparison
equal deleted inserted replaced
27:792274118b2e 28:893a6993efe3
18 user_snpdiffs_list = file("${log_directory}/Imported_SNPDiffs.txt") 18 user_snpdiffs_list = file("${log_directory}/Imported_SNPDiffs.txt")
19 findReads = file("${projectDir}/bin/fetchReads.py") 19 findReads = file("${projectDir}/bin/fetchReads.py")
20 userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py") 20 userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py")
21 21
22 // Set SKESA cores to 4 or fewer 22 // Set SKESA cores to 4 or fewer
23 skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer 23 //skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
24 skesa_cpus = 1
24 25
25 workflow { 26 workflow {
26 main: 27 main:
27 input_data = fetchData() 28 input_data = fetchData()
28 query_data = input_data.query_data 29 query_data = input_data.query_data
497 498
498 // Return assembly data 499 // Return assembly data
499 assembled_data = assembly_output.map{it->tuple(it[0],it[3])} 500 assembled_data = assembly_output.map{it->tuple(it[0],it[3])}
500 } 501 }
501 process skesaAssemble{ 502 process skesaAssemble{
502 //label 'skesaMem' 503 label 'skesaMem'
503 504
505 cpus = skesa_cpus
506
504 input: 507 input:
505 tuple val(sample_name),val(read_type),val(read_location) 508 tuple val(sample_name),val(read_type),val(read_location)
506 509
507 output: 510 output:
508 stdout 511 stdout