snakemake/snakemake-wrappers

Example Snakemake rule wrapper attribute for DADA2_QUALITY_PROFILES is incorrect

mtmcgowan opened this issue · 7 comments

mtmcgowan commented

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

fgvieira commented

Tried running the test case for that wrapper, and it works fine.
Can you give it a try?

rdenise commented

Snakemake version
Snakemake = 7.24.2
Snakemake-wrapper = v1.25.0:

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:

Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py, attempt 1/3 failed - retrying in 3 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py, attempt 2/3 failed - retrying in 6 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/v1.25.0/bio/dada2/quality-profile/wrapper.py, attempt 3/3 failed - giving up!
fgvieira commented

I tried to run the example but, even though if gave the same error, it end up founding the wrapper:

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job                         count    min threads    max threads
------------------------  -------  -------------  -------------
dada2_quality_profile_pe        1              1              1
total                           1              1              1

Select jobs to execute...

[Mon Mar 27 08:50:56 2023]
rule dada2_quality_profile_pe:
    input: trimmed/a.1.fastq, trimmed/a.2.fastq
    output: reports/dada2/quality-profile/a-quality-profile.png
    log: logs/dada2/quality-profile/a-quality-profile-pe.log
    jobid: 0
    reason: Forced execution
    wildcards: sample=a
    resources: tmpdir=/tmp

Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py, attempt 1/3 failed - retrying in 3 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py, attempt 2/3 failed - retrying in 6 seconds...
Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py
HTTPError: 404 Client Error: Not Found for url: https://github.com/snakemake/snakemake-wrappers/raw/master/bio/dada2/quality-profile/wrapper.py, attempt 3/3 failed - giving up!
Rscript --vanilla ./snakemake-wrappers/bio/dada2/quality-profile/test/.snakemake/scripts/tmpgd_lus2z.wrapper.R
Activating conda environment: .snakemake/conda/39215bc162aa14d49e07c3e5e7f3f64a_

It still fails, but with the error:

Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object './snakemake-wrappers/bio/dada2/quality-profile/test/.snakemake/conda/39215bc162aa14d49e07c3e5e7f3f64a_/lib/R/library/jpeg/libs/jpeg.so':
  libjpeg.so.9: cannot open shared object file: No such file or directory
Execution halted