Merge pull request #63 from snakemake-workflows/fix-sra-handling

fix: make specification of SRA samples in samples.tsv work (common.smk)
snakemake-workflows · Apr 13, 2023 · 5f88554 · 5f88554
2 parents 72e933b + 683c611
commit 5f88554
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -105,7 +105,7 @@ def get_fq(wildcards):
         return {"fq1": "trimmed/{sample}_{unit}_single.fastq.gz".format(**wildcards)}
     else:
         # no trimming, use raw reads
-        u = units.loc[(wildcards.sample, wildcards.unit), ["fq1", "fq2"]].dropna()
+        u = units.loc[(wildcards.sample, wildcards.unit)]
         if pd.isna(u["fq1"]):
             # SRA sample (always paired-end for now)
             accession = u["sra"]