From 939f57bdd335db23bd3ce9c136130e1cbc041a95 Mon Sep 17 00:00:00 2001
From: riasc <richard.schaefer@zoho.com>
Date: Sun, 12 May 2024 17:49:08 -0500
Subject: [PATCH] resolved typo in input rule for single-end reads

---
 workflow/rules/common.smk         | 11 +++++++++--
 workflow/rules/hlatyping.smk      |  1 +
 workflow/rules/quantification.smk |  3 +--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 39d189f..96fe9ac 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -377,7 +377,14 @@ def get_star_input(wildcards):
   elif config['data']['rnaseq_filetype'] == '.fq' or config['data']['rnaseq_filetype'] == '.fastq':
     if config['preproc']['activate']:
       if config['data']['rnaseq_readtype'] == 'SE':
-        return expand("results/{sample}/rnaseq/preproc/reads.fq.gz", **wildcards)
+        return dict(
+            zip(
+              ["fq1"],
+              expand("results/{sample}/rnaseq/reads/{group}_preproc.fq.gz",
+                      sample=wildcards.sample,
+                      group=wildcards.group)
+            )
+        )
       elif config['data']['rnaseq_readtype'] == 'PE':  # PE
         return dict(
             zip(
@@ -390,7 +397,7 @@ def get_star_input(wildcards):
         )
       else: # no pre-processing
         return config['data']['rnaseq'][wildcards.group]
-
+    
 # collect the individual alignments from splitted bamfiles
 def aggregate_aligned_rg(wildcards):
     # make sure that all samples are processed in checkpoint - split fastq file
diff --git a/workflow/rules/hlatyping.smk b/workflow/rules/hlatyping.smk
index 1995207..9393a1c 100644
--- a/workflow/rules/hlatyping.smk
+++ b/workflow/rules/hlatyping.smk
@@ -30,6 +30,7 @@ rule index_hla_panel:
     "../envs/yara.yml"
   shell:
     """
+      mkdir -p resources/hla/yara_index/
       yara_indexer \
           -o resources/hla/yara_index/{wildcards.nartype} \
           {input.fa} > {log}
diff --git a/workflow/rules/quantification.smk b/workflow/rules/quantification.smk
index 4339c46..667dd4d 100644
--- a/workflow/rules/quantification.smk
+++ b/workflow/rules/quantification.smk
@@ -48,8 +48,7 @@ rule countfeatures_rnaseq:
     sample = "results/{sample}/rnaseq/align/{group}_final_STAR.bam",
     annotation_file = "resources/refs/genome.gtf"
   output:
-    table = "results/{sample}/rnaseq/quantification/{group}_counts.txt",
-    summary = "results/{sample}/rnaseq/quantification/{group}_counts.txt.summary",
+    "results/{sample}/rnaseq/quantification/{group}_counts.txt"
   log:
     "logs/{sample}/featurecounts/rnaseq_{group}.log",
   threads: 2