From b8a280535cc3fe6c82fc05427cf885a673b868b2 Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Fri, 19 Jul 2024 16:10:51 -0400
Subject: [PATCH] loading BED from file rather than downloading via wget

---
 nextflow/main.nf                |  7 ++++++-
 nextflow/modules/rseqc/main.nf  | 12 ------------
 nextflow/subworkflows/bam_qc.nf |  7 +++----
 3 files changed, 9 insertions(+), 17 deletions(-)

diff --git a/nextflow/main.nf b/nextflow/main.nf
index d8e61ea..2f16a2d 100644
--- a/nextflow/main.nf
+++ b/nextflow/main.nf
@@ -90,6 +90,11 @@ if ( params.adapterFASTA ){
     if( !adapter_fasta.exists() ) exit 1, "Genome chrom sizes file not found: ${params.adapterFASTA}"
 }
 
+if ( params.fileBED ){
+    file_bed = file(params.fileBED)
+    if( !file_bed.exists() ) exit 1, "Bed file not found: ${params.fileBED}"
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     WORKFLOWS
@@ -130,7 +135,7 @@ workflow QC_BAM {
         .map { [it.simpleName, it ] }
         .set { bam_ch }
 
-    BAM_QC ( bam_ch )
+    BAM_QC ( bam_ch, file_bed )
 
     Channel
         .fromPath ( params.fastp_json, checkIfExists: true )
diff --git a/nextflow/modules/rseqc/main.nf b/nextflow/modules/rseqc/main.nf
index 52b0206..1f9b33c 100644
--- a/nextflow/modules/rseqc/main.nf
+++ b/nextflow/modules/rseqc/main.nf
@@ -1,15 +1,3 @@
-process GET_BED {
-    publishDir "${params.outDir}", mode: 'copy', overwrite: true
-
-    output:
-    path '*.bed*', emit: bed
-
-    shell:
-    """
-    wget -O "!{params.fileBED}" "!{params.linkBED}"
-    """
-}
-
 process RSEQC_BAMSTAT {
     label 'process_medium'
 
diff --git a/nextflow/subworkflows/bam_qc.nf b/nextflow/subworkflows/bam_qc.nf
index 65ee3fe..42e6062 100644
--- a/nextflow/subworkflows/bam_qc.nf
+++ b/nextflow/subworkflows/bam_qc.nf
@@ -1,7 +1,6 @@
 #!/usr/bin/env nextflow
 
 include { SAMTOOLS_FLAGSTAT      } from '../modules/samtools/main.nf'
-include	{ GET_BED                } from '../modules/rseqc/main.nf'
 include { RSEQC_BAMSTAT          } from '../modules/rseqc/main.nf'
 include { RSEQC_INFEREXP         } from '../modules/rseqc/main.nf'
 include { RSEQC_READDUPLICATION  } from '../modules/rseqc/main.nf'
@@ -11,14 +10,14 @@ include { RUN_MULTIQC            } from '../modules/multiqc/main.nf'
 workflow BAM_QC {
     take:
         bam       // file: /path/to/sample.bam
+        bed       // file: /path/to/bed
 
     main:
-        GET_BED()
         SAMTOOLS_FLAGSTAT ( bam )
         RSEQC_BAMSTAT ( bam )
-        RSEQC_INFEREXP ( bam, GET_BED.out.bed )
+        RSEQC_INFEREXP ( bam, bed )
         RSEQC_READDUPLICATION ( bam )
-        RSEQC_READDISTRIBUTION ( bam, GET_BED.out.bed )
+        RSEQC_READDISTRIBUTION ( bam, bed )
 
     emit:
         flagstat = SAMTOOLS_FLAGSTAT.out.flagstat