No compatible iGenomes genome for iCount peakcaller

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.

Start with main.nf lines 104 and 491, then review the iCount peakcaller path for the GRCh37 command shown in the report. Check how iGenomes references are assessed for compatibility and whether the documented manual segment-file step is expected. Done means iCount produces sample.3nt.sigxl.bed.gz and sample.3nt_3nt.peaks.bed.gz, or the documentation clearly explains the supported workaround.