From f1f1524268941f53989c11502bebc9f2fda5aed8 Mon Sep 17 00:00:00 2001
From: Lara Ianov <lianov@uab.edu>
Date: Mon, 23 Dec 2024 15:42:50 -0600
Subject: [PATCH] fixi harshil alignment and removal commented code

---
 subworkflows/local/align_longreads.nf | 4 ++--
 workflows/scnanoseq.nf                | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/align_longreads.nf b/subworkflows/local/align_longreads.nf
index aa58959..d20009d 100644
--- a/subworkflows/local/align_longreads.nf
+++ b/subworkflows/local/align_longreads.nf
@@ -3,13 +3,13 @@
 //
 
 // SUBWORKFLOWS
-include { BAM_SORT_STATS_SAMTOOLS } from '../../subworkflows/nf-core/bam_sort_stats_samtools/main'
+include { BAM_SORT_STATS_SAMTOOLS                                     } from '../../subworkflows/nf-core/bam_sort_stats_samtools/main'
 include { BAM_SORT_STATS_SAMTOOLS as BAM_SORT_STATS_SAMTOOLS_FILTERED } from '../../subworkflows/nf-core/bam_sort_stats_samtools/main'
 
 // MODULES
 include { MINIMAP2_INDEX         } from '../../modules/nf-core/minimap2/index'
 include { MINIMAP2_ALIGN         } from '../../modules/nf-core/minimap2/align'
-include { SAMTOOLS_VIEW   } from '../../modules/nf-core/samtools/view'
+include { SAMTOOLS_VIEW          } from '../../modules/nf-core/samtools/view'
 
 include { RSEQC_READDISTRIBUTION } from '../../modules/nf-core/rseqc/readdistribution/main'
 include { NANOCOMP               } from '../../modules/nf-core/nanocomp/main'
diff --git a/workflows/scnanoseq.nf b/workflows/scnanoseq.nf
index 7319e7b..7f45d43 100644
--- a/workflows/scnanoseq.nf
+++ b/workflows/scnanoseq.nf
@@ -16,9 +16,6 @@ else {
     }
 }
 
-//if (params.quantification_type.equals('both') || params.quantification_type.equals('transcript') && !params.transcript_fasta
-
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES