diff --git a/snakefile.py b/snakefile.py index a8be5ae..e6e146c 100644 --- a/snakefile.py +++ b/snakefile.py @@ -475,7 +475,8 @@ def hisat2_file_arguments(args): reads = map_input output: os.path.join(SALMON_DIR, "{sample}", "quant.sf"), - os.path.join(SALMON_DIR, "{sample}", "quant.genes.sf") + os.path.join(SALMON_DIR, "{sample}", "quant.genes.sf"), + os.path.join(SALMON_DIR, "{sample}", "libParams/flenDist.txt") resources: mem_mb = config['execution']['rules']['salmon_quant']['memory'] params: @@ -554,6 +555,7 @@ def hisat2_file_arguments(args): rule multiqc: input: salmon_output=expand(os.path.join(SALMON_DIR, "{sample}", "quant.sf"), sample = SAMPLES), + salmon_flen=expand(os.path.join(SALMON_DIR, "{sample}", "libParams/flenDist.txt"), sample = SAMPLES), mapping_output=expand(os.path.join(MAPPED_READS_DIR, MAPPER, '{sample}_Aligned.sortedByCoord.out.bam'), sample=SAMPLES) group: "qc" output: os.path.join(MULTIQC_DIR, 'multiqc_report.html')