crisprseq
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nf-core
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the...
### Description of the bug If we try to provide the count table already, we need to be able to not specify any input samplesheet, however this is leading to...
### Description of the bug The markdown table explaining the RRA contrast matrix seems to not be well formated on the nf-core website https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/rra_contrasts.txt  In addition, the example link...
### Description of feature Update the module mageck count that only has a patch in crisprseq and needs updating here : https://github.com/nf-core/modules/blob/master/modules/nf-core/mageck/count/main.nf
### Description of feature Documentation https://hackmd.io/@Fe-DlBDORpeApqPrKRTlbA/SJVrM7uHh#/1
### Description of feature Instead of using modules for the alignment step, use the nf-core subworkflows. - Use [fastq_align_bwa](https://nf-co.re/subworkflows/fastq_align_bwa) for BWA alignment - Use [fastq_align_bowtie2](https://nf-co.re/subworkflows/fastq_align_bowtie2) for bowtie2 alignemnt - Create...
### Description of the bug command: ``` nextflow run /path-to/nf-core-crisprseq-2.0.0/workflow \ -preview \ --analysis screening \ --genome GRCh37 \ -profile singularity \ --igenomes_base /path-to/references \ -offline \ --outdir . \...
### Description of feature The newly added UMI clustering steps in crisprseq targeted can be added to nf-core/modules as a subworkflow. Have a look at: - https://astro--nf-core.netlify.app/fastquorum/dev/ - https://astro--nf-core.netlify.app/subworkflows/fastq_create_umi_consensus_fgbio/
### Description of feature Create a module or multiple modules to make this script more manageable.
### Description of feature Add the functionality to analyse mock samples and remove noise from the final results.
### Description of feature Add the functionality to analyse samples with spike ins in order to remove noise from the results.