fix starfusion local module from rnafusion to migrate it to nf-core/m… #8521
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…quez/modules into fix_starfusion_local
nvnieuwk
reviewed
May 21, 2025
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+29
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+36
| wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam${pfam_version}/Pfam-A.hmm.gz --no-check-certificate | ||
| wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm --no-check-certificate | ||
| wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3f --no-check-certificate | ||
| wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3i --no-check-certificate | ||
| wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3m --no-check-certificate | ||
| wget https://www.dfam.org/releases/Dfam_${dfam_version}/infrastructure/dfamscan/${dfam_species}_dfam.hmm.h3p --no-check-certificate | ||
| gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm | ||
| wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm -O AnnotFilterRule.pm --no-check-certificate |
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I think it might be better to have these as inputs for your process. Hardcoding URLs is wildly considered to be a bad practice as the longevity of these cannot be guaranteed.
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nf-core/rnafusion#665
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda