Release version 2.2.0 with BAM and CRAM support#76
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
…into milestone_2.2.0
For milestone 2.2.0
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.
Many small fixes for milestone 2.2.0
Closes #53
Final changes for milestone 2.2.0
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Fixes for PR 76
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
JudithBernett
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JudithBernett
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lgtm! Just some minor comments
| In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. | ||
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| To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. | ||
| To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. Also please note that this pipeline uses a [Wave container](https://seqera.io/containers/) combining LAST, Samtools, and open fonts, to save the user from downloading multiple overlapping images (LAST alone, Samtools alone, LAST plus Samtools, and LAST plus open fonts). Changing this container is the simplest way to update LAST if you wish so. |
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About the wave container: Maybe it would be good to mention that they are architecture-dependent and that your wave containers are built for amd64 (right?). And that people who need arm64 (e.g., Mac users) need their own container (right?).
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I did not realise that wave containers were different from other containers in respect to arm64. Where can I find more information?
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I once asked about this on the seqera platform: https://community.seqera.io/t/platform-specificity/1116/6 , but it has been some time since then. I still don't know the best way to handle this, maybe it also does not really matter that much, I was just wondering about it :D
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Uh actually, just saw that they have something in the config:
pairgenomealign/nextflow.config
Line 122 in 9f19169
– maybe that's solved then :)
| tuple val(meta3), path(fai) | ||
| tuple val(meta4), path(gzi) |
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these parameters are unused in the file
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They are used transparently by the samtools command. Now I sort of remember that in some modules, such parameter names are prefixed with an underscore. Shall I do that at next module update?
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ahh I see :) yes, why not, or just write that in the meta.yml :)
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
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This release brings support from BAM and CRAM output formats, and allows to specify more than one format at time. It also bring a bunch of small fixes.
Version number is 2.2.0 but I wonder if it should be 3.0.0 if I take semantic versioning seriously, because I renamed one column in a TSV file output in the
alignmentsfolder, and it actually broke one of my internal pipelines that was parsing it…v2.2.0 "Chagara ponzu" - [May 29th 2025]
Added--skip_assembly_qc(#53).DependenciesSAMTOOLS_BGZIPSAMTOOLS_DICTSAMTOOLS_FAIDXParameters--skip_assembly_qcFixedMULTIQC_ASSEMBLYSCAN_PLOT_DATAlocal module (#64).multiqc_train.txtandmultiqc_last_o2o.txtaggregating alignment statistics (#52).nf-core/test-datasetsin order to run the AWS full tests (#62).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).