From bf276856b4159b0da100f33f1c1cb5f8a792e0a6 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 11:32:52 -0800
Subject: [PATCH] harmonizing with PR while that's in progress

---
 modules/nf-core/kallistobustools/count/main.nf     |  4 ++--
 modules/nf-core/kallistobustools/count/meta.yml    |  4 ++--
 .../nf-core/kallistobustools/ref/environment.yml   |  3 ++-
 modules/nf-core/kallistobustools/ref/main.nf       |  8 ++++----
 modules/nf-core/kallistobustools/ref/meta.yml      | 14 +++++++-------
 5 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 9e860241..ce5b5365 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -27,7 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
     def args    = task.ext.args ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def cdna    = t1c ? "-c1 $t1c" : ''
-    def unprocessed = t2c ? "-c2 $t2c" : ''
+    def intron  = t2c ? "-c2 $t2c" : ''
     def memory  = task.memory.toGiga() - 1
     """
     kb \\
@@ -36,7 +36,7 @@ process KALLISTOBUSTOOLS_COUNT {
         -i $index \\
         -g $t2g \\
         $cdna \\
-        $unprocessed \\
+        $intron \\
         -x $technology \\
         $args \\
         -o ${prefix}.count \\
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index c8763343..4a5d4b88 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -38,8 +38,8 @@ input:
       pattern: "*.{cdna_t2c.txt}"
   - t2c:
       type: file
-      description: kb ref's c2 unprocessed_t2c file
-      pattern: "*.{unprocessed_t2c.txt}"
+      description: kb ref's c2 intron_t2c file
+      pattern: "*.{intron_t2c.txt}"
   - workflow_mode:
       type: string
       description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml
index 62942e01..82aafedb 100644
--- a/modules/nf-core/kallistobustools/ref/environment.yml
+++ b/modules/nf-core/kallistobustools/ref/environment.yml
@@ -5,4 +5,5 @@ channels:
   - defaults
 dependencies:
   - bioconda::kb-python=0.28.2
-  - conda-forge::requests>=2.23.0
\ No newline at end of file
+  - conda-forge::requests>=2.23.0
+  
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 989f86f3..759e8663 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -17,9 +17,9 @@ process KALLISTOBUSTOOLS_REF {
     path "kb_ref_out.idx" , emit: index
     path "t2g.txt"        , emit: t2g
     path "cdna.fa"        , emit: cdna
-    path "unprocessed.fa"      , optional:true, emit: unprocessed
+    path "intron.fa"      , optional:true, emit: intron
     path "cdna_t2c.txt"   , optional:true, emit: cdna_t2c
-    path "unprocessed_t2c.txt" , optional:true, emit: unprocessed_t2c
+    path "intron_t2c.txt" , optional:true, emit: intron_t2c
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,9 +49,9 @@ process KALLISTOBUSTOOLS_REF {
             -i kb_ref_out.idx \\
             -g t2g.txt \\
             -f1 cdna.fa \\
-            -f2 unprocessed.fa \\
+            -f2 intron.fa \\
             -c1 cdna_t2c.txt \\
-            -c2 unprocessed_t2c.txt \\
+            -c2 intron_t2c.txt \\
             --workflow $workflow_mode \\
             $fasta \\
             $gtf
diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml
index 1ca31c57..0c3f78a4 100644
--- a/modules/nf-core/kallistobustools/ref/meta.yml
+++ b/modules/nf-core/kallistobustools/ref/meta.yml
@@ -45,19 +45,19 @@ output:
       type: file
       description: cDNA fasta file
       pattern: "*cdna.{fa}"
-  - unprocessed:
+  - intron:
       type: file
-      description: Unprocessed fasta file
-      pattern: "*unprocessed.{fa}"
+      description: Intron fasta file
+      pattern: "*intron.{fa}"
   - cdna_t2c:
       type: file
       description: cDNA transcript to capture file
       pattern: "*cdna_t2c.{txt}"
-  - unprocessed_t2c:
+  - intron_t2c:
       type: file
-      description: Unprocessed transcript to capture file
-      pattern: "*unprocessed_t2c.{txt}"
+      description: Intron transcript to capture file
+      pattern: "*intron_t2c.{txt}"
 authors:
-  - "@flowuenne" 
+  - "@flowuenne"
 maintainers:
   - "@flowuenne"