From f7e40f1bf22ba09168677bf47edddd5e50d84cc5 Mon Sep 17 00:00:00 2001
From: jimmyliu1326 <jimmyliu1326@yahoo.com>
Date: Fri, 31 May 2024 13:53:55 -0700
Subject: [PATCH] use nf-core/rasusa

---
 subworkflows/local/nanopore_raw_reads_qc.nf | 30 +++++++++++++--------
 subworkflows/local/raw_reads_qc.nf          |  7 +++--
 2 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/subworkflows/local/nanopore_raw_reads_qc.nf b/subworkflows/local/nanopore_raw_reads_qc.nf
index 7fec87b..9cffbe3 100644
--- a/subworkflows/local/nanopore_raw_reads_qc.nf
+++ b/subworkflows/local/nanopore_raw_reads_qc.nf
@@ -10,25 +10,33 @@ workflow NANOPORE_RAW_READS_QC {
 
     main:
     ch_versions = Channel.empty()
+    ch_qc_reads = ch_merged_reads
 
     if (!params.skip_porechop) {
         PORECHOP_ABI(ch_merged_reads)
-        ch_merged_reads = PORECHOP_ABI.out.reads
+        ch_qc_reads = PORECHOP_ABI.out.reads
     }
     if (!params.skip_subsampling) {
-        ch_genomesize = Channel.of(params.genomesize)
-
-        ch_merged_reads
-                    .combine(ch_genomesize)
-                    .set{ch_sub_reads_qc}
-
+        
+        // ch_coverages = Channel.fromList(params.depth_cut_off.split(',').collect { it.trim().toDouble() })
+
+        if (!params.skip_porechop) {
+            PORECHOP_ABI.out.reads
+                .map { meta, fastq -> 
+                    tuple(meta, fastq, params.subsampling_genomesize) 
+                }
+                .set{ch_sub_reads_qc}
+        } else {
+            ch_merged_reads
+                .map { tuple(it[0], it[1], params.subsampling_genomesize) }
+                .set{ch_sub_reads_qc}
+        }        
         RASUSA_NANOPORE(ch_sub_reads_qc, params.depth_cut_off)
-
-        ch_merged_reads = RASUSA_NANOPORE.out.reads
+        ch_qc_reads = RASUSA_NANOPORE.out.reads        
     }
     if (!params.skip_quality_report) {
         if (!params.skip_nanocomp) {
-            ch_merged_reads
+            ch_qc_reads
                 .map { [it[1]] }
                 .collect()
                 .map { reads -> [ [id: params.nanopore_summary_file_id], reads ] }
@@ -44,5 +52,5 @@ workflow NANOPORE_RAW_READS_QC {
     }
 
     emit:
-    merged_reads = ch_merged_reads
+    merged_reads = ch_qc_reads
 }
\ No newline at end of file
diff --git a/subworkflows/local/raw_reads_qc.nf b/subworkflows/local/raw_reads_qc.nf
index 2737ce0..930ba42 100644
--- a/subworkflows/local/raw_reads_qc.nf
+++ b/subworkflows/local/raw_reads_qc.nf
@@ -5,7 +5,7 @@ include { FASTQC as RAW_FASTQC     } from '../../modules/nf-core/fastqc'
 include { FASTQC as TRIM_FASTQC    } from '../../modules/nf-core/fastqc'
 include { MULTIQC as TRIM_MULTIQC  } from '../../modules/nf-core/multiqc'
 include { MULTIQC as RAW_MULTIQC  } from '../../modules/nf-core/multiqc'
-include { RASUSA                   } from '../../modules/local/rasusa'
+include { RASUSA                   } from '../../modules/nf-core/rasusa'
 include { CONFINDR                 } from '../../modules/local/confindr'
 include { AGGREGATE_CONFINDR_RESULTS                } from '../../modules/local/aggregate_confindr_results'
 include { CAT_FASTQ                } from '../../modules/nf-core/cat/fastq/main'
@@ -39,15 +39,14 @@ workflow RAW_READS_QC {
     if (!params.skip_subsampling) {
 
         ch_genomesize = Channel.of(params.subsampling_genomesize)
-        ch_coverages = Channel.fromList(params.depth_cut_off.split(',').collect { it.trim().toDouble() })
+        // ch_coverages = Channel.fromList(params.depth_cut_off.split(',').collect { it.trim().toDouble() })
 
         ch_raw_reads_qc
             .map { tuple(it[0], it[1], params.subsampling_genomesize) }
-            .combine(ch_coverages)
             .set { ch_sub_reads_qc }
             // .view()
 
-        RASUSA(ch_sub_reads_qc)
+        RASUSA(ch_sub_reads_qc, params.depth_cut_off)
 
         ch_raw_reads_qc = RASUSA.out.reads
     }