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params.config
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params.config
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params {
accessions = "Spneumoniae_SraAccList.one.txt"
/*
Component 'reads_download_1_1'
-----------------------------
*/
asperaKey_1_1 = "/Users/jcarrico/.ssh/id_rsa.pub"
/*
Component 'downsample_fastq_1_2'
-------------------------------
*/
genomeSize_1_2 = 2.1
depth_1_2 = 100
seed_1_2 = 100
clearInput_1_2 = true
/*
Component 'integrity_coverage_1_3'
---------------------------------
*/
genomeSize_1_3 = 2.1
minCoverage_1_3 = 20
/*
Component 'fastqc_trimmomatic_1_4'
---------------------------------
*/
adapters_1_4 = 'None'
trimSlidingWindow_1_4 = '5:20'
trimLeading_1_4 = 3
trimTrailing_1_4 = 3
trimMinLength_1_4 = 55
clearInput_1_4 = false
/*
Component 'check_coverage_1_5'
-----------------------------
*/
genomeSize_1_5 = 2.1
minCoverage_1_5 = 20
/*
Component 'fastqc_1_6'
---------------------
*/
adapters_1_6 = 'None'
/*
Component 'spades_1_7'
---------------------
*/
spadesMinCoverage_1_7 = 2
spadesMinKmerCoverage_1_7 = 2
spadesKmers_1_7 = 'auto'
clearInput_1_7 = true
disableRR_1_7 = false
/*
Component 'assembly_mapping_1_8'
-------------------------------
*/
minAssemblyCoverage_1_8 = 'auto'
AMaxContigs_1_8 = 100
genomeSize_1_8 = 2.1
/*
Component 'pilon_1_9'
--------------------
*/
clearInput_1_9 = true
/*
Component 'mlst_1_10'
--------------------
*/
mlstSpecies_1_10 = null
}