fix

workflow/rules/sra_download.smk

@@ -42,12 +42,12 @@ checkpoint get_layout:
  ),
  shell:
  """
- (mkdir -p {output.outdir}; \
+ (mkdir -p {output.outdir} && \
  layout=$(efetch -db sra \
  -id {wildcards.sample} \
  -format runinfo | \
- awk -F, 'x=1 NR>1 && $1 == {wildcards.sample} {print $16; x=0} END {exit x}'); \
- touch {output.outdir}/$layout.info ; \
+ awk -F, 'BEGIN {{ exitval = 1 }} NR>1 && $1 == "{wildcards.sample}" {{ print $16; exitval=0 }} END {{ exit exitval }}') && \
+ touch {output.outdir}/$layout.info; \
  ) 1> {log.stdout} 2> {log.stderr}
  """
 
@@ -87,12 +87,17 @@ def get_layouts(wildcards):
  for sample in samples[
  samples.index.str.contains("^.RR", regex=True, case=True)
  ].index.tolist():
+ layouts[sample] = []
  checkpoint_output = checkpoints.get_layout.get(
  sample=sample, **wildcards
  ).output.outdir
- layouts[sample] = glob_wildcards(
- os.path.join(checkpoint_output, "{layout}.info")
- ).layout
+ _files = [
+ os.path.join(checkpoint_output, _file)
+ for _file in os.listdir(checkpoint_output)
+ if _file.endswith(".info")
+ ]
+ assert len(_files) == 1
+ layouts[sample] = os.path.splitext(os.path.basename(_files[0]))[0]
 
  # convert layouts to short form
  layouts_short = {}
@@ -102,16 +107,16 @@ def get_layouts(wildcards):
  elif val == "SINGLE":
  layouts_short[key] = "se"
  else:
- raise ValueError("Layout not recognized.")
+ raise ValueError(f"Layout {val} for sample {key} not recognized.")
 
  # return layouts
  layouts = expand(
  os.path.join(
  config["outdir"], "compress", "{sample}", "{sample}.{seqmode}.tsv"
  ),
  zip,
- sample=ivals2.keys(),
- seqmode=ivals2.values(),
+ sample=layouts_short.keys(),
+ seqmode=layouts_short.values(),
  )
  return layouts