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nf-core
CUSTOM_DUMPSOFTWAREVERSIONS failing to parse collated_versions.yml
Description of the bug
Yet another issue with NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS, this time it is trimgalore that fails...
Command error:
INFO: Converting SIF file to temporary sandbox...
Traceback (most recent call last):
File ".command.sh", line 101, in
main()
File ".command.sh", line 61, in main
versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/__init__.py", line 81, in load
return loader.get_single_data()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/constructor.py", line 49, in get_single_data
node = self.get_single_node()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 36, in get_single_node
document = self.compose_document()
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 55, in compose_document
node = self.compose_node(None, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 133, in compose_mapping_node
item_value = self.compose_node(node, item_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/composer.py", line 127, in compose_mapping_node
while not self.check_event(MappingEndEvent):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/parser.py", line 98, in check_event
self.current_event = self.state()
^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/parser.py", line 428, in parse_block_mapping_key
if self.check_token(KeyToken):
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/scanner.py", line 116, in check_token
self.fetch_more_tokens()
File "/usr/local/lib/python3.12/site-packages/yaml/scanner.py", line 223, in fetch_more_tokens
return self.fetch_value()
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/yaml/scanner.py", line 577, in fetch_value
raise ScannerError(None, None,
yaml.scanner.ScannerError: mapping values are not allowed here
in "collated_versions.yml", line 14, column 21
INFO: Cleaning up image...
I again checked up on the collated_versions.yml file and found the following culprit:
"NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE":
trimgalore: perl: error while loading shared libraries: libperl.so: cannot open shared object file: No such file or directory
cutadapt: 3.4
The following container was used: https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0
To quick fix the error, I have modified modules/nf-core/trimgalore/main.nf, changing line 70 from:
trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
to
trimgalore: \$((trim_galore --version &>/dev/null && trim_galore --version 2>&1 | sed -n 's/^.*version \([0-9.]*\).*$/\1/p') || echo "Error")
in order to make it more robust against trim_galore --version failing for some reason. in this case it will just output "Error", and the later CUSTOM_DUMPSOFTWAREVERSIONS script will not fail to parse the YAML file...
Cheers, Martin
Command used and terminal output
No response
Relevant files
No response
System information
No response
Will be fixed in the next release (v3.15.0) because this process has already been fixed on dev.
