From eda870358696cf14175ebb898db584f14329e3aa Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 23 Oct 2023 14:07:51 -0400
Subject: [PATCH] feat: keep unpaired fastq; write stub

---
 modules/CCBR/picard/samtofastq/main.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/modules/CCBR/picard/samtofastq/main.nf b/modules/CCBR/picard/samtofastq/main.nf
index 63c7db7..7d538dc 100644
--- a/modules/CCBR/picard/samtofastq/main.nf
+++ b/modules/CCBR/picard/samtofastq/main.nf
@@ -8,7 +8,7 @@ process PICARD_SAMTOFASTQ {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.fastq"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     path "versions.yml"             , emit: versions
 
     when:
@@ -17,7 +17,7 @@ process PICARD_SAMTOFASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def output = meta.single_end ? "--FASTQ ${prefix}.fastq.gz" : "--FASTQ ${prefix}_1.fastq.gz --SECOND_END_FASTQ ${prefix}_2.fastq.gz"
+    def output = meta.single_end ? "--FASTQ ${prefix}.fastq" : "--FASTQ ${prefix}_1.fastq --SECOND_END_FASTQ ${prefix}_2.fastq --UNPAIRED_FASTQ ${prefix}.unpaired.fastq"
 
     if (!task.memory) {
         log.warn '[Picard SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -32,9 +32,17 @@ process PICARD_SAMTOFASTQ {
         --INPUT ${bam} \\
         ${output}
 
+    pigz -p ${task.cpus} *.fastq
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         picard: \$(picard SamToFastq --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+    """
 }