the output files generated by using STAR in snakemake-wrappers should be more comprehensive.

[zhongzheng1999]

I'm currently working on setting up a simple RNA-seq analysis pipeline using snakemake, and I've integrated the STAR wrapper from snakemake-wrappers. However, I've run into an issue where specifying --quantMode TranscriptomeSAM prevents me from extracting the Aligned.toTranscriptome.out.bam file as an output. I believe this file is essential for subsequent transcript quantification.

After examining the corresponding wrapper.py file, I noticed that within the with tempfile.TemporaryDirectory() as tmpdir: block, you use the cat command to output specific temporary files as result files. However, I observed that you only provided options such as ReadsPerGene.out.tab, Chimeric.out.junction, SJ.out.tab, etc., but there is no code for outputting Aligned.toTranscriptome.out.bam.

[zhongzheng1999]

When I use the --outStd BAM_SortedByCoordinate parameter, the output for {snakemake.output.aln} is the Aligned.out.bam file. However, I'm wondering if using --quantMode TranscriptomeSAM would mean that Aligned.toTranscriptome.out.bam is output instead of Aligned.out.bam. I've checked the STAR documentation but couldn't find an explanation for this issue.

[zhongzheng1999]

@kashyapchhatbar @fgvieira

[fgvieira]

From STAR's manual:

With --quantMode TranscriptomeSAM option STAR will output alignments translated into transcript coordinates in the Aligned.toTranscriptome.out.bam file (in addition to alignments in genomic coordinates in Aligned.*.sam/bam files).

So, I'd say that a new file is created. Can you double-check it?

[zhongzheng1999]

Yes, a new file is created. I modify in the local wrapper.py, gave Aligned.toTranscriptome.out.Bam one output parameter.

[fgvieira]

If you modified wrapper.py, it would be great if you could submit a PR.