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When the section name contains a special char and the plot type is table multiqc can't create the text file with the data in the temporary directory because it looks as though the file was in a subdirectory.
File that triggers the error
id: 'software_versions'section_name: 'nf-core/rnaseq Software Versions'section_href: 'https://github.com/nf-core/rnaseq'plot_type: 'table'description: 'are collected at run time from the software output.'data:
Workflow:
Nextflow: 21.04.0nf-core/rnaseq: 3.4devSTAR_ALIGN:
star: 2.6.1dTRIMGALORE:
trimgalore: 0.6.6 SALMON_TXIMPORT:
bioconductor-txmeta: 1.8.0SAMTOOLS_SORT:
samtools: 1.12STRINGTIE:
stringtie: 2.1.7SALMON_QUANT:
salmon: 1.4.0UCSC_BEDCLIP:
ucsc: 377PICARD_MARKDUPLICATES:
picard: 2.23.9SALMON_SE_GENE:
bioconductor-summarizedexperiment: 1.20.0BEDTOOLS_GENOMECOV:
bedtools: 2.30.0
MultiQC Error log
Traceback (most recent call last): │
│ File "/home/sturm/anaconda3/envs/test_multiqc/lib/python3.9/site-packages/multiqc/multiqc.py", line 624, in run │
│ output = mod() │
│ File "/home/sturm/anaconda3/envs/test_multiqc/lib/python3.9/site-packages/multiqc/modules/custom_content/custom_content.py", line 275, in custom_module_classes │
│ parsed_modules[mod_id].add_cc_section(c_id, mod) │
│ File "/home/sturm/anaconda3/envs/test_multiqc/lib/python3.9/site-packages/multiqc/modules/custom_content/custom_content.py", line 363, in add_cc_section │
│ self.write_data_file(mod["data"], "multiqc_{}".format(section_name.lower().replace(" ", "_"))) │
│ File "/home/sturm/anaconda3/envs/test_multiqc/lib/python3.9/site-packages/multiqc/modules/base_module.py", line 467, in write_data_file │
│ util_functions.write_data_file(data, fn, sort_cols, data_format) │
│ File "/home/sturm/anaconda3/envs/test_multiqc/lib/python3.9/site-packages/multiqc/utils/util_functions.py", line 69, in write_data_file │
│ with io.open(os.path.join(config.data_dir, fn), "w", encoding="utf-8") as f: │
│ FileNotFoundError: [Errno 2] No such file or directory: '/home/sturm/tmp/tmp_ubopx22/multiqc_data/multiqc_nf-core/rnaseq_software_versions.txt'
The text was updated successfully, but these errors were encountered:
Description of bug
When the section name contains a special char and the plot type is
table
multiqc can't create the text file with the data in the temporary directory because it looks as though the file was in a subdirectory.File that triggers the error
MultiQC Error log
The text was updated successfully, but these errors were encountered: