Many small fixes for milestone 2.2.0#69
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Also, the samplesheet_full.csv was updated to feature more T2T genomes. Closes #62
Closes #56 for BED support. SAM, BAM, and CRAM files are sorted for the convenience of the user, who may for instance want to index them and use them as genome browser tracks. For the BAM and CRAM files, a sequence dictionary is computed before export, to include all the sequences from the _target_ genome including those that do not have an alignment to a given _query_, so that BAM or CRAM files from multiple queries can be merged together without breaking the sort order. An assembly tag is also added, in case it is useful in the future.
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Here is a second batch of commits for milestone 2.2.0. They mainly correspond to low-hanging fruit fixes, here is a copy of the new entries in the changelog.
multiqc_train.txtandmultiqc_last_o2o.txtaggregating alignment statistics (#52).nf-core/test-datasetsin order to run the AWS full tests (#62).The next (and hopefully final) PR will be more focused and technical.
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).