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ensuring nanoplot symlinks are unique per readset #60

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Merged
MareikeJaniak merged 1 commit into from
Oct 23, 2025
Merged

ensuring nanoplot symlinks are unique per readset #60

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6 changes: 3 additions & 3 deletions genpipes/pipelines/longread_dnaseq/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ def metrics_nanoplot(self):
is_directory = False

if readset.summary_file:
input_summary = os.path.join(nanoplot_directory, os.path.basename(readset.summary_file))
input_summary = os.path.join(nanoplot_directory, f"{readset.name}.sequencing_summary.txt")
link_job = bash.ln(
os.path.abspath(readset.summary_file),
input_summary,
Expand All @@ -253,7 +253,7 @@ def metrics_nanoplot(self):
elif readset.fastq_files:
if os.path.isdir(readset.fastq_files):
is_directory = True
input_fastq = os.path.join(nanoplot_directory, os.path.basename(readset.fastq_files))
input_fastq = os.path.join(nanoplot_directory, f"{readset.name}_fastq_pass")
link_job = concat_jobs(
[
bash.rm(input_fastq),
Expand All @@ -267,7 +267,7 @@ def metrics_nanoplot(self):
input_bam = None
input_summary = None
elif readset.bam:
input_bam = os.path.join(nanoplot_directory, os.path.basename(readset.bam))
input_bam = os.path.join(nanoplot_directory, f"{readset.name}.{os.path.basename(readset.bam)}")
link_job = bash.ln(
os.path.abspath(readset.bam),
input_bam,
Expand Down