relative path for files in bin directory - address #2

AAGI-AUS · Dec 23, 2023 · 3c36fed · 3c36fed
1 parent 80965ed
commit 3c36fed
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
     """
 
 }