diff --git a/src/mapping/process_smartseq2/auto.vsh.yaml b/src/mapping/process_smartseq2/auto.vsh.yaml index 2423b2bc..3a91173d 100644 --- a/src/mapping/process_smartseq2/auto.vsh.yaml +++ b/src/mapping/process_smartseq2/auto.vsh.yaml @@ -11,11 +11,10 @@ functionality: * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`. * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`. * Write the list of samples as a yaml in the output directory. - * Map the reads using Cell Ranger - * Convert the Cell Ranger output to h5mu - * Remove ambient RNA with CellBender - * Remove cells with less than 100 genes or 1000 reads. - * Make the cell names unique + * Map the reads using Star + * Sort counts with samtools + * Convert to count table with HTSeq + * Compute QC metrics with MultiQC * Output one h5mu file per sample Concatenating the invididual h5mu files into one h5mu file is a separate pipeline.