v1.0.0

[sreichl]

• [x] Remove all donwstream analyses e.g., DeSeq & PCA
• [x] change script [count-matrix.py](http://count-matrix.py/) line 40 sep="\t" to sep = ","
• [x] switch to one sequencing unit CSV file
• [ ] change to raw BAM files as input
  • [x] alignment + downstream first
  • [ ] trimming
  • cutadapt: doesn't support unaligned paired end BAMs: https://cutadapt.readthedocs.io/en/stable/guide.html#input-and-output-file-formats
  • [ ] check if paired end does not require trimming?!
  • [ ] trimming necessary? https://github.com/alexdobin/STAR/issues/455
  • [ ] check if and how we trim in ATACseq
  • [ ] check if how BSF trims RNAseq data
  • [ ] What if it were easy and I could trim in the same step as align?
  • [ ] trimgalore
  • [ ] fastp
  • [ ] trimmomatic
• [ ] rule star_index takes very long. check if parallelizable
• [ ] test with multiple input bam files and check in dry-run shellcommands
• [ ] consider moving logs into result directory (multiqc needs to know where, ie have to change that as well)
• [ ] gene annotation including GC content and length for downstream analysis e.g., CQN normalization (code exists)
• [ ] (MultiQC) report with sequencing statistics and export as annotation (like in ATACseq)
• [ ] make README
  • [ ] Methods can be taken from macroStim
  • [ ] reference/cite the original Snakemake RNA pipeline
  • [ ] citing: If you use this workflow in a publication, please…cite this AND the original pipeline here DOI
  • [ ] citation of original pipeline in CITATION.CFF as resource
  • [ ] refer to genome_tracks module, like done in ATAC-seq pipeline (DRY principle). If group variable is sample name then its sample wise bigWigs.
• [ ] make MR.PARETO compatible

additional considerations

• [ ] (DR) TRAP_CART repo has potentially relevant code
• [ ] RtH: build in a check for paired/single-end
• [ ] DR: I forgot to clean resources folder and everything kept aligning to the downloaded genome there - important check for your version of the rna processing

[sreichl]

Resources download structure as result/ dir? ie Resources/project/module/.

Think about it and check in other workflows. If not automated download then make the recommendation of this structure.

Put into MRP module specifications