From fa9af26b4b6054225d34a566ad45bd73d921b83a Mon Sep 17 00:00:00 2001
From: lkress <35309241+LKress@users.noreply.github.com>
Date: Mon, 22 Jul 2024 10:06:13 +0000
Subject: [PATCH] Define the STAR output as bam file

---
 README.md          | 1 +
 modules/02_star.nf | 4 +++-
 nextflow.config    | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index f1851b5..1bc5bed 100755
--- a/README.md
+++ b/README.md
@@ -57,6 +57,7 @@ Optional input:
     * inception: if enabled it uses an inception, only valid for BWA aln, it requires a fast file system such as flash (default: false)
     * skip_trimming: skips the read trimming step
     * star_two_pass_mode: activates STAR two-pass mode, increasing sensitivity of novel junction discovery, recommended for RNA variant calling (default: false)
+    * star_sort_by_coordinate: Sort STAR output BAM file by coordinate (default: false)
     * additional_args: additional alignment arguments, only effective in BWA mem, BWA mem 2 and STAR (default: none) 
 
 Output:
diff --git a/modules/02_star.nf b/modules/02_star.nf
index 2f74fd0..1a6c403 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -18,6 +18,7 @@ process STAR {
 
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
+    sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : ""
     """
     STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
@@ -25,12 +26,13 @@ process STAR {
     --outSAMmode Full \
     --outSAMattributes Standard \
     --outSAMunmapped None \
+    --outSAMtype BAM ${sort} \
     --outReadsUnmapped Fastx \
     --outFilterMismatchNoverLmax 0.02 \
     --runThreadN ${task.cpus} \
     --outFileNamePrefix ${name}.
 
-    mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
+    mv ${name}.Aligned*.out.bam ${name}.bam
 
     echo ${params.manifest} >> software_versions.STAR.txt
     STAR --version >> software_versions.STAR.txt
diff --git a/nextflow.config b/nextflow.config
index 819a5b8..b7a0c27 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,6 +17,7 @@ params.memory = "32g"
 params.inception = false
 params.skip_trimming = false
 params.star_two_pass_mode = false
+params.star_sort_by_coordinate = false
 params.additional_args = ""
 params.fastp_args = ""