add updates

Author: torres-alexis

RNAseq/Pipeline_GL-DPPD-7XXX_Versions/GL-DPPD-7XXX.md

@@ -26,10 +26,10 @@ This initial release of the RNAseq pipeline documentation details the workflow s
 
 Differences with default workflow:
 - STAR is replaced with Bowtie 2 for alignment
-- RSEM is replaced with FeatureCounts for gene quantification
+- RSEM is replaced with featureCounts for gene quantification
 - kentUtils gtfToGenePred and genePredToBed are replaced with gtfToBed.py
 - rRNA genes are removed from featureCounts results on a dataset-wide basis. rRNA removal logs are all reported in the same file.
-- Rather than importing RSEM Sample.Genes.Results using tximport, the entire FeatureCounts table is imported into R for normalization and DGE analysis.
+- Rather than importing RSEM Genes.Results files for each sample using tximport, the entire FeatureCounts table is imported into R for normalization and DGE analysis.
 
 
 ---

RNAseq/README.md

@@ -3,8 +3,12 @@
 > **The document [`GL-DPPD-7101-G.md`](Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md) holds an overview and example commands for how GeneLab processes RNAseq datasets. See the [Repository Links](#repository-links) descriptions below for more information. Processed data output files and a GeneLab data processing summary is provided for each GLDS dataset in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  
 
 ---
-<img src="images/pipeline_diagram.png" align="center" alt=""/> 
-<img src="images/RNAseq_pipeline_diagram.png" align="center" alt=""/>
+RNAseq:
+<img src="images/RNAseq_eukaryotes_pipeline_diagram.png" align="center" alt=""/> 
+
+RNAseq (Prokaryotes):
+
+<img src="images/RNAseq_prokaryotes_pipeline_diagram.png" align="center" alt=""/>
 
 ---
 ## Repository Links
@@ -13,6 +17,10 @@
 
   - Contains the current and previous GeneLab RNAseq consensus processing pipeline (RCP) versions documentation
 
+* [**Pipeline_GL-DPPD-7XXX_Versions**](Pipeline_GL-DPPD-7XXX_Versions)
+
+  - Contains the current and previous GeneLab RNAseq (Prokaryotes) consensus processing pipeline (RCP) versions documentation
+
 * [**RNAseq_Tool_Install**](RNAseq_Tool_Install)
 
   - Contains instructions and associated yaml files to install the conda environments containing tools used to process RNAseq datasets using the GeneLab RCP, versions A-E

RNAseq/Workflow_Documentation/NF_RCP/CHANGELOG.md

@@ -5,12 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.0.0](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_RCP-G_2.0.0/RNAseq/Workflow_Documentation/NF_RCP-G) - 2025-01-21
+## [2.0.0](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_RCP-G_2.0.0/RNAseq/Workflow_Documentation/NF_RCP) - 2025-01-24
 
 ### Added
 
-- Microbes pipeline support via `--microbes` parameter
-  - In short, reads are aligned to a reference genome using Bowtie2 rather than STAR, gene counts are quantified using FeatureCounts rather than RSEM. Other steps remain unchanged.
+- Prokaryotes pipeline support via `--microbes` parameter
+  - In short, reads are aligned to a reference genome using Bowtie 2 rather than STAR, gene counts are quantified using featureCounts rather than RSEM. Other steps remain unchanged.
 - Unaligned reads FASTQ output from STAR
 - Variance-stabilizing transformation (VST) counts output
 - Parallel rRNA-removed DGE analysis and results. Additional 04-DESeq2_NormCounts_rRNArm/ and 05-DESeq2_DGE_rRNArm/ directories are created for rRNA-removed DGE results.

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/rseqc.nf

@@ -64,8 +64,10 @@ process INNER_DISTANCE {
 
   script:
     def log_fname = "${ meta.id }.inner_distance_freq.txt" 
+    def max_length = Math.max(150, max_read_length)
+    
     """    
-    inner_distance.py -r ${ genome_bed } -i ${ bam_file } -k ${ params.rseqc_sample_count } -l -${ max_read_length_ch } -u 350 -o ${ meta.id } 
+    inner_distance.py -r ${ genome_bed } -i ${ bam_file } -k ${ params.rseqc_sample_count } -l -${ max_length } -u 350 -o ${ meta.id } 
 
     # VERSIONS
     echo '"${task.process}":' > versions.yml

RNAseq/Workflow_Documentation/README.md

@@ -8,8 +8,9 @@ GeneLab has wrapped each step of the pipeline into a workflow with validation an
 
 |Pipeline Version|Current Workflow Version (for respective pipeline version)|Nextflow Version|
 |:---------------|:---------------------------------------------------------|:---------------|
-|*[GL-DPPD-7101-F.md](../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md)|[NF_RCP-F_1.0.4](NF_RCP-F)|22.10.1|
-|*[GL-DPPD-7101-G.md](../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md)|[NF_RCP-G_2.0.0](NF_RCP-G)|24.10.3|
+|*[GL-DPPD-7101-F.md](../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md)|[NF_RCP-F_1.0.4](https://github.com/nasa/GeneLab_Data_Processing/tree/NF_RCP-F_1.0.4/RNAseq/Workflow_Documentation/NF_RCP-F)|22.10.1|
+|*[GL-DPPD-7101-G.md](../Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md)|[NF_RCP-G_2.0.0](NF_RCP)|24.10.3|
+|*[GL-DPPD-7XXX.md](../Pipeline_GL-DPPD-7XXX_Versions/GL-DPPD-7XXX.md)|[NF_RCP-X_2.0.0](NF_RCP)|24.10.3|
 
 *Current GeneLab Pipeline/Workflow Implementation