Have you checked the docs?
Description of the bug
Description of the bug
The prokka module in nf-core/modules is using a Conda environment specification that allows GNU Parallel to update to version 20260422 (latest), which causes failures when processing certain annotations. This issue specifically occurs when Conda-based CI tests are launched.
The problem has been identified and fixed in the nf-core/bacass pipeline (PR #303) by pinning GNU Parallel to version 20241122 (conda-forge::parallel=20241122), matching the version used in the Docker/Wave container.
Error message:
Could not run command: cat TestMe\-miniasm\-medaka\/TestMe\-miniasm\-medaka\.proteins\.tmp\.10301\.faa | parallel --gnu --plain -j 2 --block 1950 --recstart '>' --pipe blastp -query - -db TestMe-miniasm-medaka/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > TestMe\-miniasm\-medaka\/TestMe\-miniasm\-medaka\.proteins\.tmp\.10301\.blast 2> /dev/null
Command used and terminal output
Relevant files
No response
System information
No response
Have you checked the docs?
Description of the bug
Description of the bug
The
prokkamodule in nf-core/modules is using a Conda environment specification that allows GNU Parallel to update to version 20260422 (latest), which causes failures when processing certain annotations. This issue specifically occurs when Conda-based CI tests are launched.The problem has been identified and fixed in the nf-core/bacass pipeline (PR #303) by pinning GNU Parallel to version 20241122 (
conda-forge::parallel=20241122), matching the version used in the Docker/Wave container.Error message:
Could not run command: cat TestMe\-miniasm\-medaka\/TestMe\-miniasm\-medaka\.proteins\.tmp\.10301\.faa | parallel --gnu --plain -j 2 --block 1950 --recstart '>' --pipe blastp -query - -db TestMe-miniasm-medaka/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > TestMe\-miniasm\-medaka\/TestMe\-miniasm\-medaka\.proteins\.tmp\.10301\.blast 2> /dev/nullCommand used and terminal output
Relevant files
No response
System information
No response