Define the STAR output as bam file

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:

modules/02_star.nf

@@ -18,19 +18,21 @@ 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" \
     --readFilesIn ${fastq1} ${fastq2} \
     --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

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 = ""