fix: quantification input output mismatch (#68)

* fix: aligned rule count_reads output iwth rule merge_counts input

* fix: added dir parameter again because output no longer a dir

workflow/rules/quantification.smk

@@ -7,8 +7,9 @@ rule count_reads:
         bam="sorted_alignments/{sample}.bam",
         trs="transcriptome/transcriptome.fa",
     output:
-        tsv=directory("counts/{sample}_salmon"),
+        tsv="counts/{sample}_salmon/quant.sf",
     params:
+        tsv_dir="counts/{sample}_salmon",
         libtype=config["salmon_libtype"],
     log:
         "logs/salmon/{sample}.log",
@@ -17,7 +18,7 @@ rule count_reads:
     shell:
         """
         salmon --no-version-check quant --ont -p {resources.cpus_per_task} \
-        -t {input.trs} -l {params.libtype} -a {input.bam} -o {output.tsv} 2> {log}
+        -t {input.trs} -l {params.libtype} -a {input.bam} -o {params.tsv_dir} 2> {log}
         """