Fix mismatching names for cluster config and Snakefile

[alexg9010]

See https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/128#issuecomment-2034898830

• [x] hisat2-build --> hisat2_index

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/snakefile.py#L356-L363

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/etc/settings.yaml.in#L94

[alexg9010]

• [x] trim_qc_reads --> trim_qc_reads_pe, trim_qc_reads_se

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/snakefile.py#L318-L341

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/etc/settings.yaml.in#L88

[alexg9010]

• [x] hisat2 --> hisat2_map

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/snakefile.py#L402-L409

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/etc/settings.yaml.in#L115

[alexg9010]

• [ ] counts_from_salmon --> counts_from_SALMON

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/snakefile.py#L468-L479

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/etc/settings.yaml.in#L103

[borauyar]

@alexg9010 would you like to fix the issue and send a pull request?

[alexg9010]

@alexg9010 would you like to fix the issue and send a pull request?

Just finishing up the collection.

[alexg9010]

• [x] report --> report1/2/3, deseq_collate_report1/2/3

https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/bd38e02d499fa93ef44f95aaf3b5c4c8c636a19c/snakefile.py#L591-L627