Pipeline (7101-G and 7115) and workflow updates (v2.0.0) #154

bnovak32 · 2025-05-20T21:35:52Z

Bulk RNASeq Pipeline updates:

update to version G for eukaryotes (GL-DPPD-7101),
add GL-DPPD-7115 for prokaryotes

Workflow updates:

add support for pipelines GL-DPPD-7101-G and GL-DPPD-7115.
update software and reference database versions
refactor V&V code
fix issues [BulkRNASeq] V&V program mistypes samplenames as ints when possible #33, [BulkRNASeq] Workflow fails to launch using approach 3 when gldsAccession is not supplied #35, [BulkRNASeq] Underspecification of memory for STAR_ALIGN #36, Add reference table support for "Pseudomonas Aeruginosa" #37, [BulkRNASeq] Remove generation of visualization extended DGE table #41, [BulkRNASeq] Add V&V Check: Assert adaptor content removed using Trimmed Reads FastQC MultiQC #42, [BulkRNASeq] Generate CSV of parsed metrics #84, [BulkRNASeq] VV_DESEQ2_ANALYSIS error with all integer sample names #112

Update GL-DPPD-7101-G.md

- Add inputs and outputs for Step 9 sections - fix annotations table lines

Add updated RNAseq (eukaryotic pipeline): GL-DPPD-7101-G.md and new RNAseq prokaryotic pipeline

- Add featurecounts module - Make multiQC PE sample merging recognize only "_R1" and "_R2" suffixes - fix gtf_to_bed.py - fix align_bowtie2.nf - fix build_bowtie2_index.nf - add samtools stats

- Rename and gzip unmapped fastq outputs

Misc fixes

fixed underscore typo

remove "R1" from single-end unmapped.fastq.gz suffix

Set validation mode to lenient to allow number input for input parameters with string type (for example "--genome_version 112")

Moved ADD_GENE_ANNOTATIONS and ADD_GENE_ANNOTATIONS_RRNA_RM from 1CPU/2GB RAM section to 4CPU/16GB RAM section in local.config and slurm.config

torres-alexis and others added 30 commits January 21, 2025 11:23

disable conda on nf profile

d167320

microbes doc draft

bc9585c

update doc

024968b

fix order of DGE table columns

2bbb75d

rm doc

36f43eb

clarify tech reps handling

7d24135

add updates

e5b4a39

update copyright year

4ac179b

add bowtie2 alignment

20161fa

add star align exit

4086561

typo fix

8ff9b12

add up to bowtie

4540927

reorder pipelines

011d7fa

fix readme

8fe2072

update pipeline number

6c92e0e

update pipeline references

77dbf72

Update GL-DPPD-7101-G.md

44b7898

Merge pull request #21 from asaravia-butler/patch-1

d003cae

Update GL-DPPD-7101-G.md

pipeline doc edits

cf6bde3

Updates to RNAseq pipeline document

c05bfa0

- Add inputs and outputs for Step 9 sections - fix annotations table lines

change groups wording

c4c895f

rnaseq doc updates

1867a12

fix dge table gene annotation cols ordering

c06ba5b

Merge pull request #138 from torres-alexis/DEV_RNAseq_vG_CURRENT

dd68d0c

Add updated RNAseq (eukaryotic pipeline): GL-DPPD-7101-G.md and new RNAseq prokaryotic pipeline

RNAseq (Prokaryotes)

1071eca

- Add featurecounts module - Make multiQC PE sample merging recognize only "_R1" and "_R2" suffixes - fix gtf_to_bed.py - fix align_bowtie2.nf - fix build_bowtie2_index.nf - add samtools stats

add microbes partial doc

6d13c92

fix gtf to bed

ed57d45

add prokaryotes pipeline doc draft

3690af4

fix versions

936a719

update rnaseq microbes docs

3f37b20

torres-alexis and others added 30 commits April 29, 2025 18:14

add tech reps line, fix syntax in ending, in generated protocol

747505a

vv bowtie2 alignment - account for empty unmapped fastq

f884699

STAR alignment: add --genomeLoad LoadAndKeep

30730e3

move new align_star parameter above read Ins

d7c3cc0

change genomeload from loadandkeep to loadandremove

4d08619

RNAseq: reduce resource allocations

7986bba

Add slurm executor settings

d71970c

Update build_star_index limitGenomeGenerateRam allocation

55f66a2

RNAseq - update resource allocations

094bc73

RNAseq slurm - increase submitRateLimit

c0e044e

vv dge - explicitly set sample names as string

eecf3b6

update changelog

6d07013

increase align star mem

a963cc5

Move parse annotations table color defs to exec block

aac1d52

Change parse_annotations_table to script block

3c278a3

convert parse_annotations_table module to a subworkflow

84eeaa1

move parse annotations table to modules

84acd74

- ALIGN_STAR: finalize genomeLoad setting for use with 2-pass

c8f2bcc

- Rename and gzip unmapped fastq outputs

make local.config match slurm.config

043d191

add generate_md5sums to config

f69a322

Remove _R1 suffix from unmapped SE read filename

c1e6603

finish SE unmapped reads name fixes

367ca56

remove unused sort_into_subdirectories_by_sample.py

89a4039

Allow integer sample names in input runsheet

8a2a38a

Allow integer sample names - finished

d178627

Merge pull request #148 from torres-alexis/null_annotations_bug_fix

e2a7ff2

Misc fixes

Update align_star.nf

921d40e

fixed underscore typo

Update update_assay_table.py

908d338

remove "R1" from single-end unmapped.fastq.gz suffix

Update nextflow.config

8c7835c

Set validation mode to lenient to allow number input for input parameters with string type (for example "--genome_version 112")

Update resource allocation for ADD_GENE_ANNOTATION processes (#155)

4bc0dc5

Moved ADD_GENE_ANNOTATIONS and ADD_GENE_ANNOTATIONS_RRNA_RM from 1CPU/2GB RAM section to 4CPU/16GB RAM section in local.config and slurm.config

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Pipeline (7101-G and 7115) and workflow updates (v2.0.0) #154

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bnovak32 commented May 20, 2025

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Pipeline (7101-G and 7115) and workflow updates (v2.0.0) #154

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Pipeline (7101-G and 7115) and workflow updates (v2.0.0) #154

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bnovak32 commented May 20, 2025

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