Release 2.3 Updates: Fixes for contamination, UMI Handling, Template 2.11.1 #303
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Reverting changes to a non-linted version and added the umitools modules.
Added the umitools workflow and integrated it into the smrnaseq workflow
Add additional documentation to use UMI tools as part of the pipeline. Most of the documentation has been copied from nf-core/rnaseq.
The bam2fq module is neccessary to convert the deduplicated bam files back into a fastq format to be fed into the existing pipeline.
Added the umitools extract modules.config lines from nf-core/rnaseq to this pipeline.
Added configurations for umi deduplication.
Initial comit of the umi dedup subworkflow. The workflow combines already existing modules of the pipeline and nf-core module to deduplicate the reads by mapping them to the species genome and re-converting them to fastq after deduplication.
includes the optional umitools deduplication step after the read QC.
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.
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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@nf-core-bot fix linting |
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Related to #114
PR checklist
nf-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).