From b0c2f875f7b0723cbe43341ccf6757b9f2a51d7e Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 29 Oct 2024 10:43:25 +0100
Subject: [PATCH] Refactor output directory structure

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 bin/fastqc.sh          | 7 +++----
 main.nf                | 2 +-
 modules/fastqc/main.nf | 4 ++--
 modules/quant/main.nf  | 4 ++--
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/bin/fastqc.sh b/bin/fastqc.sh
index 93f38b6..8138193 100755
--- a/bin/fastqc.sh
+++ b/bin/fastqc.sh
@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
-sample_id="$1"
-reads="$2"
+reads="$1"
 
-mkdir fastqc_${sample_id}_logs
-fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
+mkdir fastqc
+fastqc -o fastqc -f fastq -q ${reads}
diff --git a/main.nf b/main.nf
index 8ce4333..ba2bca2 100755
--- a/main.nf
+++ b/main.nf
@@ -73,7 +73,7 @@ workflow {
 
 output {
   samples {
-    path '.'
+    path { id, _quant, _fastqc -> "${workflow.outputDir}/${id}" }
     index {
       path 'index.json'
       mapper { id, quant, fastqc ->
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index cb960be..abd06f7 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -7,10 +7,10 @@ process FASTQC {
     tuple val(sample_id), path(fastq_1), path(fastq_2)
 
     output:
-    tuple val(sample_id), path("fastqc_${sample_id}_logs"), emit: logs
+    tuple val(sample_id), path('fastqc')
 
     script:
     """
-    fastqc.sh "$sample_id" "$fastq_1 $fastq_2"
+    fastqc.sh "$fastq_1 $fastq_2"
     """
 }
diff --git a/modules/quant/main.nf b/modules/quant/main.nf
index 027f9d5..a53fedf 100644
--- a/modules/quant/main.nf
+++ b/modules/quant/main.nf
@@ -8,10 +8,10 @@ process QUANT {
     tuple val(sample_id), path(fastq_1), path(fastq_2)
 
     output:
-    tuple val(sample_id), path(sample_id)
+    tuple val(sample_id), path('quant')
 
     script:
     """
-    salmon quant --threads $task.cpus --libType=U -i $index -1 ${fastq_1} -2 ${fastq_2} -o $sample_id
+    salmon quant --threads $task.cpus --libType=U -i $index -1 ${fastq_1} -2 ${fastq_2} -o quant
     """
 }