From 40e97e2c672efb1da578a4480f5a16210b99d288 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Wed, 12 Jun 2024 12:24:21 -0700
Subject: [PATCH] merge with sfitz-by-readgroup complete and tested

---
 main.nf                   | 4 ++--
 module/fastqc.nf          | 6 +++---
 test/config/fastqc.config | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index f823b63..433de5c 100755
--- a/main.nf
+++ b/main.nf
@@ -162,9 +162,9 @@ workflow {
             samples_to_process_ch
             )
         }
-    if ('fastqc' in params.algorithms) {
+    if ('fastqc' in params.algorithm) {
         assess_ReadQuality_FastQC(
-            samplesToProcessChannel
+            samples_to_process_ch
             )
         }
     if ('collectwgsmetrics' in params.algorithm) {
diff --git a/module/fastqc.nf b/module/fastqc.nf
index 2f285d9..707d126 100644
--- a/module/fastqc.nf
+++ b/module/fastqc.nf
@@ -14,10 +14,10 @@ process assess_ReadQuality_FastQC {
         pattern: "${output_filename}",
         mode: "copy",
         enabled: true
-    ext log_dir_suffix: { "-${id}" }
+    ext log_dir_suffix: { "-${sm_id}" }
 
     input:
-        tuple val(orig_id), val(id), path(path), val(read_length), val(sample_type)
+        tuple path(path), val(unused), val(sm_id), val(rg_arg), val(unused), val(unused), val(unused), val(read_length)
 
     output:
         path("${output_filename}")
@@ -25,7 +25,7 @@ process assess_ReadQuality_FastQC {
     script:
     output_filename = generate_standard_filename("FastQC-${params.fastqc_version}",
         params.dataset_id,
-        id,
+        sm_id,
         [:])
 
     """
diff --git a/test/config/fastqc.config b/test/config/fastqc.config
index d460f83..dce8944 100644
--- a/test/config/fastqc.config
+++ b/test/config/fastqc.config
@@ -8,7 +8,7 @@ includeConfig "${projectDir}/nextflow.config"
 
 // Inputs/parameters of the pipeline
 params {
-    algorithms = ['fastqc']
+    algorithm = ['fastqc']
     reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
     blcds_registered_dataset = false // if you want the output to be registered
     save_intermediate_files = true