ylab-hi / scanneo2 Goto Github PK
View Code? Open in Web Editor NEWSnakemake-based computational workflow for neoantigen prediction from diverse sources
License: MIT License
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scanneo2's Issues
Add routine to catch missing input data on filesystem
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
Paired-end Bam files causes error exception in featureCounts
nthreads cannot be larger than environment variable
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)
MHC-I genotyping on Split BAMs
BAMfiles probably need to be QNAME sorted (rather than coordinate sorted) when splitting them
GATK Speedup Gather&Scatter
Input should be splitted by chromosome...
Slow FTP download of VEP Cache
Related to Ensembl/ensembl-vep#1332
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