This is a rnaseq data processing pipeline based on the one in
https://github.com/ewels/nf-core-rnaseq
which is really nice nf pipeline.
Some customized modification has been done to adapt the IMP/IMBA slurm HPC
- add the intron length parameter for star aligner and test it
- add the single-end reads for feature counts
- add the index .bai.bai files for the aligned bams from star
- change the base.config to adapt ii2
- some quality control steps need to be turned off:
- skip_genebody_coverage --skip_dupradar --skip_edger --sampleLevel --skip_multiqc
in which the gene_body_coverage, dupradar and edgr and sample_corrrelation are turned off
- multiqc is also turned off, because the multiqc can not manage for big number of samples