From 658471f58f75a868bc3261596148374440b183bd Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Sun, 29 Sep 2024 14:23:44 -0300
Subject: [PATCH] refact: Allow using refs from GenCode

commit 88282b8ba196ab28e886fc45b671634f498b500a
Author: jvfe <jvfecav@gmail.com>
Date:   Sun Sep 29 13:53:22 2024 -0300

    fix: Add missing dot to regex

commit 5efc0b43f555e276b9ba6fec99e2ceaa1aeaab5e
Author: jvfe <jvfecav@gmail.com>
Date:   Sun Sep 29 10:56:45 2024 -0300

    refact: Try handling bars in IDs
---
 bin/gen_tx2gene.r | 3 +++
 bin/tximport.r    | 3 +++
 nextflow.config   | 2 +-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/bin/gen_tx2gene.r b/bin/gen_tx2gene.r
index 1c18ea2..dfcb854 100755
--- a/bin/gen_tx2gene.r
+++ b/bin/gen_tx2gene.r
@@ -26,6 +26,9 @@ txdf <- AnnotationDbi::select(
 tab <- table(txdf$GENEID)
 txdf$ntx <- tab[match(txdf$GENEID, names(tab))]
 
+txdf$TXNAME <- gsub("\\..*", "",  txdf$TXNAME)
+txdf$GENEID <- gsub("\\..*", "",  txdf$GENEID)
+
 tx2gene <- data.frame(
     tx = txdf$TXNAME,
     gene = txdf$GENEID
diff --git a/bin/tximport.r b/bin/tximport.r
index 1ba0b7c..e5c5cfa 100755
--- a/bin/tximport.r
+++ b/bin/tximport.r
@@ -20,6 +20,7 @@ txi_gene <- tximport(
     type = "kallisto",
     tx2gene = tx2gene,
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )
 
@@ -28,6 +29,7 @@ txi_tx <- tximport(
     type = "kallisto",
     txOut = TRUE,
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )
 
@@ -37,6 +39,7 @@ txi_tx_scaled <- tximport(
     txOut = TRUE,
     countsFromAbundance = "scaledTPM",
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )
 
diff --git a/nextflow.config b/nextflow.config
index 7cc2c1e..d4dadac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -195,7 +195,7 @@ manifest {
     description     = 'Workflow for pre-processing, alignment and quantification of bulk RNA-Seq data'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '0.5.0'
+    version = '0.6.0'
     doi             = ''
 }