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Example Snakemake rule wrapper attribute for DADA2_QUALITY_PROFILES is incorrect #622
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Tried running the test case for that wrapper, and it works fine. |
Snakemake version Description of the bug I encountered the same problem rule dada2_quality_profile_pe:
input:
# FASTQ file without primer sequences
expand(os.path.join(
OUTPUT_FOLDER,
"databases",
"reads_trimmed",
"paired",
"{{sample}}_R{orientation}.fastq.gz",
),
orientation=[1,2]
)
output:
os.path.join(
OUTPUT_FOLDER,
"reports",
"dada2",
"quality-profile",
"{sample}-quality-profile.png"
)
log:
os.path.join(
OUTPUT_FOLDER,
"logs",
"dada2",
"quality-profile",
"{sample}-quality-profile.log"
)
wrapper:
"v1.25.0/bio/dada2/quality-profile" It said that it tried to find the Python wrapper and not the R wrapper:
|
I tried to run the example but, even though if gave the same error, it end up founding the wrapper:
It still fails, but with the error:
|
This issue was marked as stale because it has been open for 6 months with no activity. |
I think that what is happening is that If so, it is just a bit misleading error message... |
Snakemake version
Snakemake = 7.16.0
Snakemake-wrapper = v1.17.3
Describe the bug
Using the example wrapper attribute for DADA2_QUALITY_PROFILES ("v1.17.3/bio/dada2/quality-profile") causes a 404 error when Conda tries to pull the wrapper file.
The http link that causes the 404 error appears like it points to a python wrapper instead of an R wrapper.
Updating the wrapper attribute in my Snakefile to "v1.17.3/bio/dada2/quality-profile/wrapper.R" appears to solve the problem.
Logs
Did not collect logs
Minimal example
rule dada2_quality_profile_pe:
input:
expand("{project_dir}/{sample_name}-{rep}_{orientation}_001.fastq.gz",
project_dir=config['project_dir'],
orientation=[1, 2],
allow_missing=True)
output:
"reports/dada2/quality-profile/{sample_name}-{rep}-quality-profile.png"
log:
"reports/dada2/quality-profile/{sample_name}-{rep}-quality-profile.log"
wrapper:
"v1.17.3/bio/dada2/quality-profile"
Additional context
None
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