nf-core/tools: v2.1 - Zinc Zebra

Template Correct regex pattern for file names in nextflow_schema.json Remove . from nf-core/tools command examples Update Nextflow installation link in pipeline template (#1201) Command hostname is not portable [#1212] Changed how singularity and docker links are written in template to avoid duplicate links General Changed names of some flags with -r as short options to make the flags more consistent between commands. Modules Added consistency checks between installed modules and modules.json (#1199) Added support excluding or specifying version of modules in .nf-core.yml when updating with nf-core modules install --all (#1204) Created nf-core modules update and removed updating options from nf-core modules install Added missing function call to nf-core lint (#1198) Fix nf-core lint not filtering modules test when run with --key (#1203) Fixed nf-core modules install not working when installing from branch with -b (#1218) Added prompt to choose between updating all modules or named module in nf-core modules update Check if modules is installed before trying to update in nf-core modules update Verify that a commit SHA provided with --sha exists for install/update commands Add new-line to main.nf after bump-versions command to make ECLint happ