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Commit 8254361f authored by Simeon's avatar Simeon
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bugged funannotate integration

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/home/nibio/Documents/Git/DivGene-genome-annotation/work/b2/4d0430cc99d9679f13bbc44fdb2b14/MinP1831_erik_protein.fa
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/home/nibio/Documents/Git/DivGene-genome-annotation/work/3c/48d999464a895324d779655902e4b4/MinP1831_erik_em.emapper.annotations
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/home/nibio/Documents/Git/DivGene-genome-annotation/work/e3/b57eac02db62ca9e83c859e498918e/fixed.gff
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/home/nibio/Documents/Git/DivGene-genome-annotation/work/d9/759832a0f6ff7f32cf96c6610b9246/MinP1831_erik_interpro.xml
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library(effectR)
# fasta_prot <- seqinr::read.fasta(commandArgs(trailingOnly = TRUE)[1])
test <- seqinr::read.fasta("Mid_test_data/nextflow_results/MidP1831_erik_protein.fa")
fasta_prot <- test
rxlr_cand <- regex.search(fasta_prot)
crn_cand <- regex.search(fasta_prot, motif = "CRN")
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params.genome = "MidP1831_erik"
params.project = "/home/nibio/Documents/Git/DivGene-genome-annotation/Mid_test_data"
params.genome = "MinP1831_erik"
params.project = "/home/nibio/Documents/Git/DivGene-genome-annotation/Min_test_data"
profiles {
conda {
......
......@@ -80,7 +80,7 @@ publishDir "${params.project}/nextflow_results/interpro", mode: 'symlink'
~/interproscan-5.68-100.0/interproscan.sh \
-i $proteinFasta \
-f xml \
-b "${params.genome}_interpro.xml"
-b "${params.genome}_interpro"
"""
}
......@@ -113,9 +113,10 @@ funannotate annotate \
workflow {
def gff_ch = Channel.fromPath(params.genomeGFF)
def sp_ch = Channel.value(params.speciesStrain)
fixGFF(gff_ch)
extractProteins(params.genomeFasta, fixGFF.out)
searchAndAnnotateEggnogg(extractProteins.out)
searchAndAnnotateInterPro(extractProteins.out)
funannotateIntegration(fixGFF.out, params.genomeFasta, searchAndAnnotateEggnogg.out, searchAndAnnotateInterPro.out, params.sbt, params.speciesStrain)
funannotateIntegration(fixGFF.out, params.genomeFasta, searchAndAnnotateEggnogg.out, searchAndAnnotateInterPro.out, params.sbt, "Pinf")
}
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