missing readspergene out with new wrapper
rule align_multi:
input:
# this function is called as many samples are provided in output
# technical replicates are merged in STAR
fq1 = get_fq1,
fq2 = get_fq2, # optional, return none if not in units.tsv
idx = rules.star_index.output
output:
aln="star/{sample}/Aligned.sortedByCoord.out.bam",
log="logs/star/{sample}/Log.out",
log_final="logs/se/{sample}/Log.final.out",
sj="star/{sample}/SJ.out.tab",
reads_per_gene= "star/{sample}/ReadsPerGene.out.tab"
log:
"logs/star/{sample}.log"