[pull] master from nf-core:master#54
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pull[bot] merged 8 commits intoBatoolMM:masterfrom May 22, 2025
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* migrate bam_tumor_only_somatic_variant_calling_gatk tests * remove old tests files * update tests and snapshots * code polish
…o nf-test (#8527) * Migrate to nf-test * Fix lint * Add bcftools plugin fill tags * Update meta.yml * Update test * Fix test * Update test * Update nf-test * Add bedtools stub test * Update pluginfilltags test * Update modules/nf-core/bcftools/pluginfilltags/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/bcftools/pluginfilltags/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Set to input * Update meta.yml * Update argument to nf-test * Update argument * Update pluginfilltags test --------- Co-authored-by: LouisLeNezet <louislenezet@gamil.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
* Add Antismash with new container (NO TESTS YET) * Update downloaddatabases * Add doickerfile * Update snapshot file so more explicitly show output * Clean up snap and add deprecation messag eto old antismashlite modules * Add missing deprecation message * Apply suggestions from code review * Update -*lit tests to acount for deprecation * Apply suggestions from code review Co-authored-by: Niklas Schandry <schandry@gmail.com> Co-authored-by: Martín Beracochea <mbc@ebi.ac.uk> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> * Address more of @nschan's commnets * Update README.md * Apply suggestions from code review --------- Co-authored-by: Niklas Schandry <schandry@gmail.com> Co-authored-by: Martín Beracochea <mbc@ebi.ac.uk> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com>
* Added module * updated module * Updated testdata * Updated msisensorpro to v1.3.0 * Removed files for pro command * Updated snapshot * Updated msisensorpro/msisomatic * Updated conda to v1.3.0, fixed linting * Added optional flag to germline and somatic output
…ed. (#8512) * Change the way the sequence dictionary and the read groups are produced. The sequence dictionary is now made by `samtools dict`. This ensures that sequences not part of the alignment are also listed. This is essentional for further merge operations on the SAM/BAM/CRAM files. Another benefit of `samtools dict` is that it allows to provide a relative URL to the genome file in the samtools header. To preserve this URL during the call to `samtools sort`, EBI querying is disabled. In addition `maf-convert` is now used to output read groups, therefore allowing us remove one samtools step. * Get the sequence dictionary from the input… … instead of potentially re-computing it many times for the same genome sequence. Thanks, @maxulysse for the heads-up.
* Add a gzi input channel to `samtools/merge` This is needed because `samtools merge --reference genome.fa.gz` fails when not provided a `genome.fa.gz.gzi` file… * Create a new test instead of modifying old one. As requested by @maxulysse
* add cowpy * more tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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