No compatible iGenomes genome for iCount peakcaller

[irikas]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/clipseq pipeline documentation

Description of the bug

iCount peakcaller cannot be used with iGenomes reference genome. This is referenced in line 104 of main.nf:
icount_compatible = [] // Currently none of the iGenomes GTFs are compatible (even Ensembl - as different to the ones downloaded directly from Ensembl)

This makes using the iCount peakcaller difficult as it requires manual generation of the iCount segment file (line 491: iCount segment $gtf icount_${gtf} $fai)

The run will still complete successfully after STEP 7 - Identify crosslinks

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/clipseq --input $INPUT_DIR/input_design.csv --outdir $OUT_DIR --genome GRCh37 --move_umi XXNNN --peakcaller iCount --motif true --max_cpus 28 --max_time 72.h --email $EMAIL_IS -profile singularity
2. See error: WARN: The provided genome 'GRCh37' is not compatible with the iCount peakcaller, so it will be skipped. Please see documentation

Expected behaviour

Peak calling using iCount - generation of sample.3nt.sigxl.bed.gz and sample.3nt_3nt.peaks.bed.gz files

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware: HPC
• Executor: slurm
• OS: GNU/Linux
• Version 4.18.0-477.21.1.el8_8.x86_64

Nextflow Installation

• Version: 22.10.6

Container engine

• Engine: Singularity
• version: 3.8.7
• Image tag: nf-core/clipseq v1.0.0�

Additional context

Not sure if this is purposeful and there is an expected workaround.