Refactor output directory structure

Signed-off-by: Ben Sherman <[email protected]>

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}

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 ->

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"
     """
 }

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
     """
 }