Barbara Novak

Some datasets can have over 1,000 files in the MAGs and bins folders of the Assembly-based_processing directories (for example: https://genelab-tools.arc.nasa.gov/jira/browse/GLDATAPROC-694). There's no need to have all of them available individually.

The pipeline specifies coordinate-sorted BAM as input for deduplicated_bismark (see [GL-DPPD-7113 Step 6](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md#6-deduplicate-skip-if-data-are-rrbs)), but the deduplicate_bismark tool requires readname sorted input files (see [Bismark documentation](http://felixkrueger.github.io/Bismark/bismark/deduplication/)).

* Updated Amplicon Seq pipeline doc - add zipped files and zip steps - rarefaction_depth.txt files - assay_suffix added throughout - sync alpha/beta diversity code - failure file notes -...

- Regularize indentation/spacing in code blocks - Add note at top about tech_type and assay suffixes.

[bulkRNASeq] NF_RCP 2.0.0 - post-processing fails after with user-provided runsheet_path

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**Describe the bug** Post-processing workflow fails on run folder created by main workflow that was started with a run sheet rather than an accession number. **To Reproduce** Steps to reproduce...

[bulkRNASeq] NF_RCP 2.0.0 - Custom genomes are limited to organisms found in reference_table

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**Describe the bug** Custom genome support is limited to organisms found in the pre-defined `reference_table` **To Reproduce** Steps to reproduce the behavior: 1. Run the NF_RCP 2.0.0 main workflow on...