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In ran on the star 2.7.1a star aligner. The option --chimOutType is not set correctly when I ran it showed me the conflict options.
https://github.com/ylab-hi/ScanNeo2/blob/main/workflow/rules/align.smk#L33C1-L33C34

EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions
SOLUTION: re-run with --chimOutType Junctions

However, the pipeline already sets with --chimOutType WithinBAM HardClip.
Currently, I replace the option as recommended automatically by the software.
Can you check on the current smk align rule. If it is not set correctly, please update the pipeline.

When I ran spladder in the altsplicing task. It is lacked of parallel option that slows the process.
https://github.com/ylab-hi/ScanNeo2/blob/main/workflow/rules/altsplicing.smk#L17C1-L24C39
Just add --parallel <cpus>

Related to Ensembl/ensembl-vep#1332

The workflow/envs/optitype.yml environment is limited to NUMEXPR_MAX_THREADS" (64). This applies only when setting the threads number higher than 64.

Error.  nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)

Needs to be either increased or limited to 64 (hla typing)

Missing input data causes:

MissingInputException in rule fastqc_forward in file /projects/b1171/sej9799/GBM_analysis/ScanNeo2/workflow/rules/preproc.smk, line 35:
Missing input files for rule fastqc_forward:
output: results/SRR8281248/rnaseq/qualitycontrol/rna_tumor_R1_fastqc_raw.html, results/SRR8281248/rnaseq/qualitycontrol/rna_tumor_R1_fastqc_raw.zip
wildcards: sample=SRR8281248, seqtype=rnaseq, group=rna_tumor
affected files:
../GBM/SRR8281248_1.fastq

Should be caught differently

BAMfiles probably need to be QNAME sorted (rather than coordinate sorted) when splitting them

From the .tests/integration/config_basic/config.yaml
Do you know how I can get these files to test it?
TESLA_9_2.fastq.gz
TESLA_10_2.fastq.gz
TESLA_11_2.fastq.gz

Input should be splitted by chromosome...