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Add filterScore and sjdOverhangMin parameters #136

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merged 9 commits into from
Jun 26, 2020
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Updated indentation of all parameters in config
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PhilPalmer committed Jun 26, 2020
commit f23ce485f6c2da3ba086af750c000e29b7dde411
58 changes: 29 additions & 29 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -6,45 +6,45 @@ manifest {

params {
// Input files
reads = false
bams = false
rmats_pairs = false
download_from = false
key_file = false
reads = false
bams = false
rmats_pairs = false
download_from = false
key_file = false

// Main arguments:
gtf = false
assembly_name = false
star_index = false
singleEnd = false
stranded = 'first-strand'
readlength = false
gtf = false
assembly_name = false
star_index = false
singleEnd = false
stranded = 'first-strand'
readlength = false

// Trimmomatic:
minlen = 20
slidingwindow = true
adapter = false
minlen = 20
slidingwindow = true
adapter = false

// Star
overhang = false
mismatch = 2
filterScore = 0.66
sjdOverhangMin = 8
overhang = false
mismatch = 2
filterScore = 0.66
sjdOverhangMin = 8

// rMATS
statoff = false
paired_stats = false
novelSS = false
mil = 50
mel = 500
statoff = false
paired_stats = false
novelSS = false
mil = 50
mel = 500

// Other
test = false
skiprMATS = false
skipMultiQC = false
outdir = 'results'
multiqc_config = "$baseDir/examples/assets/multiqc_config.yaml"
help = false
test = false
skiprMATS = false
skipMultiQC = false
outdir = 'results'
multiqc_config = "$baseDir/examples/assets/multiqc_config.yaml"
help = false
}

process {
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