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nextflow.config
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params {
// Sample specification and input data directory
sample_manifest = "$baseDir/resources/samples/samples.csv"
bam_folder = "$baseDir/data"
// where to place results
results = "$baseDir/results"
// Setting for specific steps of the workflow
pbaa_resources = "$baseDir/resources/pbaa"
classify_resources = "$baseDir/resources/classify"
// Reference files for vsearch orient step
dpa_reference = "$baseDir/resources/orient/MW679627.fasta"
dpb_reference = "$baseDir/resources/orient/MW679628.fasta"
dqa_reference = "$baseDir/resources/orient/MW679620.fasta"
dqb_reference = "$baseDir/resources/orient/MW679622.fasta"
drb_reference = "$baseDir/resources/orient/MW679619.fasta"
// Settings for trimming step
dpa_minimum_length = "2300"
dpa_forward_primers = "GTRTGCTATGTATTTGCTTCATAGGG"
dpa_reverse_primers = "GGGTAAGAGGTTAGATATGGGAGT"
dpb_minimum_length = "5700"
dpb_forward_primers = "GGATTAGGTGAGAGTGGYGCC"
dpb_reverse_primers = "TAGGTCATGTTTGTTCCCCGAC,CCTGAGTACTTGGGACCTCATG"
dqa_minimum_length = "1900"
dqa_forward_primers = "GGTTCTTTCTTCCCCTGTTCTCC"
dqa_reverse_primers = "ATAGTTTCAGTCAGCCCTGGATG"
dqb_minimum_length = "4000"
dqb_forward_primers = "AGARCGCCCTGATCCCTCTAA"
dqb_reverse_primers = "YACCAAAGTTAAGGCTTGGTTCT"
drb_minimum_length = "3500"
drb_forward_primers = "GCGTCGCTGTCAGTGTCTTC"
drb_reverse_primers = "TTCCTCCTCCAGAAAAGCCTATGG,AACCATGCACTGATSATTTCTGGA"
// Settings for PBAA
dpa_guide_fasta = "$baseDir/resources/pbaa/MW679627.fasta"
dpb_guide_fasta = "$baseDir/resources/pbaa/MW679628.fasta"
dqa_guide_fasta = "$baseDir/resources/pbaa/MW679620.fasta"
dqb_guide_fasta = "$baseDir/resources/pbaa/MW679622.fasta"
drb_guide_fasta = "$baseDir/resources/pbaa/cy0333-drb.fasta"
// Annotate files
dpa_mrna_reference = "$baseDir/resources/annotate/MW679627-e2-e4-mRNA.fasta"
dpa_cds_annotation = "$baseDir/resources/annotate/MW679627-e2-e4-mRNA-annotations.txt"
dpb_mrna_reference = "$baseDir/resources/annotate/MW679628-e2-e4-mRNA.fasta"
dpb_cds_annotation = "$baseDir/resources/annotate/MW679628-e2-e4-mRNA-annotations.txt"
dqa_mrna_reference = "$baseDir/resources/annotate/MW679620-e2-e4-mRNA.fasta"
dqa_cds_annotation = "$baseDir/resources/annotate/MW679620-e2-e4-mRNA-annotations.txt"
dqb_mrna_reference = "$baseDir/resources/annotate/MW679622-e2-e4-mRNA.fasta"
dqb_cds_annotation = "$baseDir/resources/annotate/MW679622-e2-e4-mRNA-annotations.txt"
drb_mrna_reference = "$baseDir/resources/annotate/MW679619-e2-e4-mRNA.fasta"
drb_cds_annotation = "$baseDir/resources/annotate/MW679619-e2-e4-mRNA-annotations.txt"
}
// Docker settings
docker.enabled = true
process.container = 'dockerreg.chtc.wisc.edu/dhoconno/mhc-alleles-from-gdna-amplicons:27751'
// Changing default workflow-visualizing configuration to true
dag {
enabled = true
overwrite = true
file = 'mhc-class2-allele-discovery.png'
}
// Workflow introspection
timeline {
enabled = false
// overwrite = true
file = "${params.results}/timeline.html"
}
report {
enabled = false
// overwrite = true
file = "${params.results}/report.html"
}
trace {
enabled = false
// overwrite = true
fields = 'task_id,name,status,exit,realtime,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar'
file = "${params.results}/trace.txt"
}