From 3c36feddcedc969dada6028fd9d2d0979c295b62 Mon Sep 17 00:00:00 2001
From: KristinaGagalova <kristina.gagalova@curtin.edu.au>
Date: Sat, 23 Dec 2023 18:48:53 +0800
Subject: [PATCH] relative path for files in bin directory - address #2

---
 modules/module_align_counts.nf | 5 ++---
 modules/module_align_qc.nf     | 5 ++---
 modules/module_read_cont.nf    | 2 +-
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/modules/module_align_counts.nf b/modules/module_align_counts.nf
index 519141e..525bcfb 100644
--- a/modules/module_align_counts.nf
+++ b/modules/module_align_counts.nf
@@ -19,9 +19,8 @@ process combine_counts_star {
 
     script:
     """
-    ./bin/CombineCounts-star.py --input $counts --strandedness $strandedness --output RawCountsStar.tsv
+    CombineCounts-star.py --input $counts --strandedness $strandedness --output RawCountsStar.tsv
     """
-
 }
 
 process combine_counts_featurecounts {
@@ -37,7 +36,7 @@ process combine_counts_featurecounts {
 
     script:
     """
-    ./bin/CombineCounts-featurecounts.py --input $counts --output RawCountsFeatureCounts.tsv
+    CombineCounts-featurecounts.py --input $counts --output RawCountsFeatureCounts.tsv
     """
 
 }
diff --git a/modules/module_align_qc.nf b/modules/module_align_qc.nf
index 989a9e5..6cd4271 100644
--- a/modules/module_align_qc.nf
+++ b/modules/module_align_qc.nf
@@ -17,7 +17,7 @@ process convert_bed {
 
     script:
     """
-    ./bin/gtf2bed.py $genes | awk -F'\t' 'NF==12 {print}' > ${genes.simpleName}.bed12
+    gtf2bed.py $genes | awk -F'\t' 'NF==12 {print}' > ${genes.simpleName}.bed12
     """
 }
 
@@ -114,7 +114,6 @@ process combine_bam_stats {
 
     script:
     """
-    ./bin/Combine-bam-stats.py --input $bam_stats --output StatsBam.tsv
+    Combine-bam-stats.py --input $bam_stats --output StatsBam.tsv
     """
-
 }
diff --git a/modules/module_read_cont.nf b/modules/module_read_cont.nf
index aab3acb..d9ff5db 100644
--- a/modules/module_read_cont.nf
+++ b/modules/module_read_cont.nf
@@ -16,7 +16,7 @@ process combine_cont_bbt {
 
     script:
     """
-    $PWD/bin/CombineCont.py --input $rates --output ContaminationRate.tsv
+    CombineCont.py --input $rates --output ContaminationRate.tsv
     """
 
 }