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* Template update for nf-core/tools version 3.4.1 * Template update for nf-core/tools version 3.4.1 * move params * changelog * Drocrate * snap * contriv * Apply suggestion from @maxulysse Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * Apply suggestion from @maxulysse Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * disable tower * skip fastqc * skip fastqc * snap --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Remove fastqc * Run pre-commit --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
* Add citations * Run pre-commit * Update CITATIONS.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
* Get PCGR reference automatically * change containers * add pcgr/getref * add pcgr/getref * update module inputs * add download * handle vep cahce * pre-commit * use nf-core module * cleanup * remove unused module * test * add snap for swbf and remove unused conf * adjust test memory limit * Update schema * change config * try using other genome for test * hard code genome to test * hard code genome to test * try cache from raredisease * try with untar * revert change to samplesheet * sawp * use NCBI igenome * swap to GATK * swap to GATK * Add VEP Cache for chr22 * current state * it workds * Add vep cache * rescue versions * update snap * use downsampled PCGR * fix linting * Add vcf assertion
* Add citations * Run pre-commit * Update CITATIONS.md Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Add test utils and default test * Apply suggestions from code review * Apply suggestion from @famosab * Apply suggestion from @famosab * Apply suggestion from @famosab --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Retrieve PCGR db and VEP cache automatically
* Template update for nf-core/tools version 3.4.1 * Template update for nf-core/tools version 3.5.1 * Template update for nf-core/tools version 3.5.1 * Small fixes * Update changelog * run nextflow lint * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestions from code review --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Move test data to repo and add full_size test config * Changelog * Add full_size snap and tag for CI-tests * Apply suggestion from @famosab
* More changes to adhere to strict syntax * syntax * fix one more error * bump schema * bump schema
* Recover help message * changelog
Expand and adapt documentation
…format_input-modules enable conda usage for the entire pipeline
* Template update for nf-core/tools version 3.3.2 * Template update for nf-core/tools version 3.5.2 * rocrate * fix input schema * revert not needed changes * recover README * Apply suggestion from @famosab * rocrate
Restructure local modules
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Recover PCGR output, swap to topics
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Still missing CPSR implementation and version bump but opening now to check whether the CI tests run through!