[RELEASE PR for 2.3.0 release] #305
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Added additional configuration to change the output file name of samtools sort.
Added the documentation detailing the output files of the UMI-tools deduplication step.
After deduplication the reads that remained unaligned to the provided reference genome are merged with the set of deduplicated reads to enable the use of the full spectrum of reads, independent of potential reference bias. This behaviour can be deactivated by setting --umi_merge_unmapped false
Information on the new --umi_merge_unmapped command were added to both the CHANGELOG, as well as the output markdown script.
Includes the nf-core cat module to replace the custom concatenation module.
Implements the use of the nf-core cat module.
deletes the now unused conatenation module.
Fix bowtie index issue
…-2.13Apply chris changes on top
nvnieuwk
approved these changes
Feb 23, 2024
Co-authored-by: Christopher Mohr <contact.cmohr@gmail.com>
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Will also wait for @christopher-mohr 's final words. And running a few combination tests locally on our HPC to be safe. These few hours are not going to hurt anymore ;-) |
maxulysse
reviewed
Feb 23, 2024
maxulysse
reviewed
Feb 23, 2024
maxulysse
reviewed
Feb 23, 2024
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PR checklist
Full Changelog:
v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian
genome_quant.r)three_prime_adapterper defaultParameters
--with_umi--umitools_extract_method--umitools_method--skip_umi_extract--umitools_bc_pattern--umi_discard_read--save_umi_intermeds--save_aligned--save_aligned_mirna_quant--save_mergedSoftware dependencies
multiqcedgeRlimmabioconvertmirdeepseqkitfastqcsamtoolsumitoolsumicollapsenf-core lint).nextflow run . -profile 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).