From 8254361f34ba6037e69cecb2b5f219afd95a72bf Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Fri, 14 Jun 2024 15:10:11 +0200
Subject: [PATCH] bugged funannotate integration
---
Min_test_data/nextflow_results/MinP1831_erik_protein.fa | 1 +
.../emapper/MinP1831_erik_em.emapper.annotations | 1 +
Min_test_data/nextflow_results/fixed.gff | 1 +
.../nextflow_results/interpro/MinP1831_erik_interpro.xml | 1 +
effector_annot.r | 8 ++++++++
nextflow.config | 4 ++--
pinf_genome_annotation.nf | 5 +++--
7 files changed, 17 insertions(+), 4 deletions(-)
create mode 120000 Min_test_data/nextflow_results/MinP1831_erik_protein.fa
create mode 120000 Min_test_data/nextflow_results/emapper/MinP1831_erik_em.emapper.annotations
create mode 120000 Min_test_data/nextflow_results/fixed.gff
create mode 120000 Min_test_data/nextflow_results/interpro/MinP1831_erik_interpro.xml
create mode 100644 effector_annot.r
diff --git a/Min_test_data/nextflow_results/MinP1831_erik_protein.fa b/Min_test_data/nextflow_results/MinP1831_erik_protein.fa
new file mode 120000
index 0000000..55f9c3b
--- /dev/null
+++ b/Min_test_data/nextflow_results/MinP1831_erik_protein.fa
@@ -0,0 +1 @@
+/home/nibio/Documents/Git/DivGene-genome-annotation/work/b2/4d0430cc99d9679f13bbc44fdb2b14/MinP1831_erik_protein.fa
\ No newline at end of file
diff --git a/Min_test_data/nextflow_results/emapper/MinP1831_erik_em.emapper.annotations b/Min_test_data/nextflow_results/emapper/MinP1831_erik_em.emapper.annotations
new file mode 120000
index 0000000..a167931
--- /dev/null
+++ b/Min_test_data/nextflow_results/emapper/MinP1831_erik_em.emapper.annotations
@@ -0,0 +1 @@
+/home/nibio/Documents/Git/DivGene-genome-annotation/work/3c/48d999464a895324d779655902e4b4/MinP1831_erik_em.emapper.annotations
\ No newline at end of file
diff --git a/Min_test_data/nextflow_results/fixed.gff b/Min_test_data/nextflow_results/fixed.gff
new file mode 120000
index 0000000..7530602
--- /dev/null
+++ b/Min_test_data/nextflow_results/fixed.gff
@@ -0,0 +1 @@
+/home/nibio/Documents/Git/DivGene-genome-annotation/work/e3/b57eac02db62ca9e83c859e498918e/fixed.gff
\ No newline at end of file
diff --git a/Min_test_data/nextflow_results/interpro/MinP1831_erik_interpro.xml b/Min_test_data/nextflow_results/interpro/MinP1831_erik_interpro.xml
new file mode 120000
index 0000000..8def519
--- /dev/null
+++ b/Min_test_data/nextflow_results/interpro/MinP1831_erik_interpro.xml
@@ -0,0 +1 @@
+/home/nibio/Documents/Git/DivGene-genome-annotation/work/d9/759832a0f6ff7f32cf96c6610b9246/MinP1831_erik_interpro.xml
\ No newline at end of file
diff --git a/effector_annot.r b/effector_annot.r
new file mode 100644
index 0000000..d57afb1
--- /dev/null
+++ b/effector_annot.r
@@ -0,0 +1,8 @@
+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")
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 50bbaf2..2dec088 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,5 +1,5 @@
-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 {
diff --git a/pinf_genome_annotation.nf b/pinf_genome_annotation.nf
index 1ae7ee7..4e25b99 100644
--- a/pinf_genome_annotation.nf
+++ b/pinf_genome_annotation.nf
@@ -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")
}
\ No newline at end of file
--
GitLab