Remove path from modules - address #2

AAGI-AUS · Dec 23, 2023 · 6e09ac5 · 6e09ac5
1 parent 08c1319
commit 6e09ac5
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/main.nf b/main.nf
@@ -180,9 +180,9 @@ workflow GENOME_INDEX {
 	run_hisat_index_high_mem(genome, genes)
      } else if (aligner == "hisat") {
 	run_hisat_index(genome, genes) 
-     } else if (aligner == "star")  {
+     } else if (aligner == "star" || || aligner == "star-plants")  {
 	run_star_index(genome, genes)
-     } else if (aligner == "star-snps" || aligner == "star-plants") {
+     } else if (aligner == "star-snps") {
 	run_star_index_snps(genome, genes)
      }
 }

diff --git a/modules/module_align_counts.nf b/modules/module_align_counts.nf
@@ -19,7 +19,7 @@ process combine_counts_star {
 
     script:
     """
-    $PWD/bin/CombineCounts-star.py --input $counts --strandedness $strandedness --output RawCountsStar.tsv
+    ./bin/CombineCounts-star.py --input $counts --strandedness $strandedness --output RawCountsStar.tsv
     """
 
 }
@@ -37,7 +37,7 @@ process combine_counts_featurecounts {
 
     script:
     """
-    $PWD/bin/CombineCounts-featurecounts.py --input $counts --output RawCountsFeatureCounts.tsv
+    ./bin/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:
     """
-    $PWD/bin/gtf2bed.py $genes | awk -F'\t' 'NF==12 {print}' > ${genes.simpleName}.bed12
+    ./bin/gtf2bed.py $genes | awk -F'\t' 'NF==12 {print}' > ${genes.simpleName}.bed12
     """
 }
 
@@ -114,7 +114,7 @@ process combine_bam_stats {
 
     script:
     """
-    $PWD/bin/Combine-bam-stats.py --input $bam_stats --output StatsBam.tsv
+    ./bin/Combine-bam-stats.py --input $bam_stats --output StatsBam.tsv
     """
 
 }