Fix: Adding batch id to prevent overwrite of counts matrix.

Author: skchronicles

workflow/Snakefile

@@ -128,8 +128,8 @@ rule all:
         # transcripts option is provided.
         # @imported from rules/isoformswitchanalyzer.smk
         # @output of rule isoformswitchanalyzer_salmon_matrix
-        provided([join(workpath, "counts", "salmon.transcripts.raw_counts.tsv")], quantify_transcripts != "None"),
-        provided([join(workpath, "counts", "salmon.transcripts.tpm_normalized.tsv")], quantify_transcripts != "None"),
+        provided([join(workpath, "counts", batch_id, "salmon.transcripts.raw_counts.tsv")], quantify_transcripts != "None"),
+        provided([join(workpath, "counts", batch_id, "salmon.transcripts.tpm_normalized.tsv")], quantify_transcripts != "None"),
         # Create comparisons sample sheet for running ISA
         # conditionally runs if the quantify
         # transcripts option is provided and

workflow/rules/isoformswitchanalyzer.smk

@@ -163,8 +163,8 @@ rule isoformswitchanalyzer_salmon_matrix:
     input:
         counts = expand(join(workpath, "counts", "transcripts", "{name}", "quant.sf"), name=samples),
     output:
-        raw = join(workpath, "counts", "salmon.transcripts.raw_counts.tsv"),
-        tpm = join(workpath, "counts", "salmon.transcripts.tpm_normalized.tsv"),
+        raw = join(workpath, "counts", batch_id, "salmon.transcripts.raw_counts.tsv"),
+        tpm = join(workpath, "counts", batch_id, "salmon.transcripts.tpm_normalized.tsv"),
     params:
         rname  = "salmonmatrix",
         tmpdir = join(workpath, "temp"),