Comments (1)
Hi @AASTHAPAL9
sorry for getting back to you so late! Is there any chance you could run it with docker instead of conda? We're experiencing some difficulties:
nextflow run nf-core/crisprseq -r 2.1.1 --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --library final_input_sgrna.tsv --analysis screening --outdir /home/ap764/mageck/output -profile docker
let me know if this is possible :)
from crisprseq.
Related Issues (20)
- --reference and --protospacer not working
- Process exceeded running time limit (8h) HOT 1
- Please pin the version of the `nf-validation` plugin!
- cutadapt needs to be adapted to fit both screening and targeted workflows HOT 1
- Copy original file rather than softlink HOT 6
- Add seperate R scripts for local modules
- Pass BAGEL2 in conda
- error in NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE file is not in PNG format HOT 4
- N characters introduced into *indels.csv HOT 7
- ZeroDivisionError at alignment_summary.py stage due to low read number in input: mapped_reads_percentage = mapped_reads_count * 100 / total_reads_count
- Improve documentation describing day0 label HOT 1
- Suggested addition: a PCA illustrating sample/condition/replicates
- Output link on website is broken, directs to wrong url
- MAGeCK is pulling conditions instead of unique sample names
- MAGECK mle cnv correction doesn't work HOT 4
- No such variable CUTADAPT (v.2.2.0) HOT 6
- Check if the matrice creation works properly
- Sample not being detected as edited despite evidence of editing in the bam file HOT 1
- Pass DRUGZ in conda
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