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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Update GL-DPPD-7115.md
- Added missing input definition in 9e - Reverted accidental deletion of the end of the Workflow README.
…pad build_star memory
- fixed arrow connections
- fixes DGE group stats calculation - Update pipeline docs with DGE group stats calculation fix - fix arrows in workflow images
…o add_custom_organisms
- Updated Workflow Changelog to capture latest changes - added "ignore" as the errorStrategy for UPDATE_ASSAY_TABLE so that it exits gracefully rather than breaking the post-processing workflow.
- Unzip local reference fasta/gtf that are gzipped (same as for URL download)
Rna seq add custom organisms
Updated dp_tools version.
Updated dp_tools version.
Updated dp_tools version
Contributor
Author
|
Only remaining typos and broken links detected in RNASeq subdirectory are in previous pipeline/workflow versions. |
bnovak32
added a commit
to bnovak32/GeneLab_Data_Processing
that referenced
this pull request
Aug 14, 2025
commit 335518184cd9fa8a615ff03890bca72423d0112f
Merge: f3da4eb bc388dd
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 14:21:21 2025 -0700
RNASeq workflow 2.0.1 patch update
- Fixed qc_metrics generation
- Added qc_metrics documentation
commit bc388dd2d240edd3118279eacb27e9dfb67e281c
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 14:18:38 2025 -0700
Fix link in Changelog
commit 394ac1f1233cad9e68c88ac6273b7b1749c614e0
Merge: 819c6d9 ac0caea
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 14:14:16 2025 -0700
Merge pull request #167 from asaravia-butler/DEV_RNAseq_vG
Updating definitions
commit ac0caeae834e434ca1b0355c500058187a3cb6a4
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Wed Jul 2 14:01:42 2025 -0700
Updating definitions
commit 819c6d906e1c17018f70333abd45d6a26a51d9a3
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 10:50:16 2025 -0700
updated qc_metrics documentation
commit d73c4eb69fac5a5f0e4ded5affdbaa17b1567eec
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 10:49:07 2025 -0700
fixed "tss_down" typo
commit 1647aa9227449c4f15602dc629562204b01093da
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed Jul 2 10:25:16 2025 -0700
Added QC metrics definitions
commit f766a5609bac0447df8017503814875940a6ed87
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Tue Jul 1 09:44:41 2025 -0700
Added workflow documentation of QC metrics output
commit 4fd24e21ac201c9d24f1c2224441dea11bf45d0a
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 30 16:52:32 2025 -0700
Updated changelog
commit 1d3fa6667615e5d6b40ed75c7f21c17377eb05b6
Merge: 36ead3d cbe694c
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 30 16:43:15 2025 -0700
Merge pull request #165 from torres-alexis/DEV_RNAseq_vG
- Fixed fastqc parsing in parse_multiqc.py
- Updated documentation with new version number
- Added validation output file for parse_multiqc.py
commit cbe694c7a98d374f5cdfd41aeef660d07a9465ef
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Jun 27 21:07:04 2025 -0700
Adjust parse qc report text to use jira syntax
commit 14ff32278675f4836bf067362c2e5799540a8a8b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 18:49:18 2025 -0700
typo fix
commit 0f4f326f9a41194fd3bad26a7be47da245613c59
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 18:36:49 2025 -0700
Add validation text file output to parse_multiqc.py
commit 24b3c0e9e7299a7546c73776d5028a555fafa8fd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 17:37:08 2025 -0700
Add runsheet ordering to qc_metrics
commit 8a3d385e9c51f2cc2d68fdb11b8a082be6e70959
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 17:25:30 2025 -0700
Switch out fastqc indexing for content check in parse qc script
commit be376e055aa7536dd718a70a82beb3faa0934706
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 15:01:28 2025 -0700
Update documentation for NF-RCP 2.0.1
commit 9c55e72e4dfad1bb3dc72edf26becc085c007b05
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 15:00:04 2025 -0700
Update nextflow manifest version to 2.0.1
commit e388f75de022054a372c740245dec826e8e15a33
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Jun 26 14:33:25 2025 -0700
Fix incorrect index for cutadapt multiqc parsing
commit f3da4eb19c1733422351664bb10e4d27049e6e08
Merge: 296943b 36ead3d
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:55:28 2025 -0700
Merge pull request #154 from nasa/DEV_RNAseq_vG
RNASeq Pipeline (7101-G and 7115) and workflow updates (NF_RCP v2.0.0)
commit 36ead3dcdf748596208004a862eda03182037494
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:49:59 2025 -0700
more typo fixes
commit d7183ddf51dbdb52871182d71f18ddb73ab07dcd
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:39:33 2025 -0700
Typo fixes
commit ab4eb3217c56bbb50764037e0eb78c67ad5b4deb
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:05:21 2025 -0700
Update CHANGELOG.md
Updated dp_tools version
commit 228c40b2d6ece439a03482a33f49c1dee8b2acc7
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:03:41 2025 -0700
Update GL-DPPD-7115.md
Updated dp_tools version.
commit bbeefb48189b0ff50404f3a7a1565c63ed4e98b1
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 15:03:03 2025 -0700
Update GL-DPPD-7101-G.md
Updated dp_tools version.
commit 29000df1b989e01660b8f90af4cebacbddb11c02
Merge: ea083fd 39f38c7
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 14:59:24 2025 -0700
Merge pull request #160 from bnovak32/RNASeq_add_custom_organisms
Rna seq add custom organisms
commit 39f38c7bb5fd91f26d4e763831cbf1d11d0e5e33
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 9 14:55:21 2025 -0700
Updated reference download to properly deal with gz files
- Unzip local reference fasta/gtf that are gzipped (same as for URL
download)
commit 0350b1cc7422e914b1574bb4432d1b6f24270d20
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Fri Jun 6 17:24:00 2025 -0700
update CHANGELOG and escape for UPDATE_ASSAY_TABLE
- Updated Workflow Changelog to capture latest changes
- added "ignore" as the errorStrategy for UPDATE_ASSAY_TABLE so that it
exits gracefully rather than breaking the post-processing workflow.
commit c16efb4e4206d133d6d7e30ff68d6511f614d4a8
Merge: ea083fd 3216f87
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Fri Jun 6 11:54:34 2025 -0700
Merge remote-tracking branch 'torres-alexis/add_custom_organisms' into add_custom_organisms
commit ea083fd77ad577799ffa7d63ad1f6d05723afa13
Merge: 4bc0dc5 f8dc1b0
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Jun 5 10:51:57 2025 -0700
Merge pull request #158 from torres-alexis/dge_stats
- fixes DGE group stats calculation
- Update pipeline docs with DGE group stats calculation fix
- fix arrows in workflow images
commit f8dc1b0de55e25cb217befe204fc81b1cd755584
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Jun 5 10:40:09 2025 -0700
updated dates to match Jira
commit 457b920ffbb2931511dd28d077dfb996339c7b20
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Jun 5 10:30:26 2025 -0700
updated pipeline images
- fixed arrow connections
commit 3019d9e18c1041d0f57bd4342abf1fe58190effc
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Jun 4 11:46:10 2025 -0700
generate protocol - update tech reps section
commit a338a7b72c722b7bd72322f60e51b5dd3d7d86a6
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Jun 4 09:34:05 2025 -0700
Update microbes protocol assembly source line
commit 9e429b3f46c349565a829de2658115dfbe16f2a4
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 18:11:55 2025 -0700
Add DGE tech rep handling logic accounting for 'Has Tech Reps' column
commit dffbb6eda0761fe378b50000b85be5959b83c6e3
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 18:00:00 2025 -0700
Add secondary runsheet publishing location for runsheet based runs
commit dbbf3946482bbe0aebf79070bfa45f2fb0644bb5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 17:59:40 2025 -0700
Update dp tools plugin for 'Has Tech Reps' column
commit f3a4368af82c5163aebd893783b352bc357db6f0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 16:59:55 2025 -0700
Add secondary isa archive publishing for isa_archive_path runs
commit 23e222b7e39ad385554c52884d50ff76880fb065
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 16:10:39 2025 -0700
fix params typo
commit 114b3bc04ccd45a8898b4e439f293292aedca19d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 13:35:00 2025 -0700
add ram disclaimer to fetch singularity images
commit 8a59259170b96f2d62d6dba3f2d1bcd0166bac2c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 13:17:37 2025 -0700
Improve Has Tech reps column description
commit 91027c18266682084b2ff17819a1779f3c17cca5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 13:16:46 2025 -0700
Remove Source Name definition
commit 9d4e68462dc97d3e95d135487945ff942ed5b5e5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 13:06:17 2025 -0700
Update runsheet examples readme and runsheets
commit 513f6871df22d6630fd076673036694889c62362
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 12:46:04 2025 -0700
add gene annotations script: move output dir creation to set up block
commit f58edee707a65b6be92ca9d5084def45554beb10
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Jun 3 11:43:07 2025 -0700
Increase default star alignment memory to resolve memory limit fail; pad build_star memory
commit c6b53925d94dea6e3d509250c1d9ddc2821a965b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Jun 2 21:04:33 2025 -0700
Update assay table - remove addition of 'Has Tech Rep' column functionality
commit 59b235c429dd4d5cbf8ba73bec55242257f35428
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Mon Jun 2 10:42:30 2025 -0700
Minor pipeline and workflow readme fixes
- Added missing input definition in 9e
- Reverted accidental deletion of the end of the Workflow README.
commit b6e6c0d76f5a147e58b9e8209b63c8d7913f6f06
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 17:40:14 2025 -0700
Adjust resource allocations, add to readme
commit 9fa67bd408ad499974c163abf7e48c36fc8e9b09
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 17:07:33 2025 -0700
Readd --no-home setting for singularity profile
commit b6c55274f9259657ff917600fdcc302a7eb5dc4b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 17:05:00 2025 -0700
add local profile to nextflow run command examples in readme
commit 9d6c41a3374c3827f7db17474527851859d574e0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 13:11:04 2025 -0700
generate protocol - add gene IDs vs ENSEMBL IDs in rRNArm line based on ref source
commit 1e98f1b7c519d6fdac4c8f5366e1335e4a3766eb
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 12:45:22 2025 -0700
Fix to not include yellow flag lines in vv_log_final_only_issues
commit 00a8a5c0f1c5a8989ffca3f2add266991bcb2409
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 02:37:45 2025 -0700
update generated protocol
commit ed0e20ab04740e1d9b9442ce0c7e752131028c73
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 02:21:15 2025 -0700
Update dp tools to 1.3.8, add source name and tech rep column to runsheet, add tech rep col to assay table
commit a5ea17754c6b41e517e9e6bb7d7e810157a9c2c8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 30 01:26:22 2025 -0700
Update assay table - Fix issue where Inner Distance Files would be added for SE
commit 422903a5246354a44ac517a4a5fbb1909ddb51f1
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 29 13:18:31 2025 -0700
add random seed to dge script
commit 83411ce0359792e425dcb3d5227beb536b98c7d7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 29 10:36:40 2025 -0700
Fix output directory creation in dge script
commit 4d380df82726eda530f8a356f900c9a72c33088a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 29 09:50:01 2025 -0700
Make Source Names col optional in DGE, update docs, fix docs
commit e9d7ecc45b98ecdd13c421684e370e48ff7e6266
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 29 00:08:25 2025 -0700
DGE - Handle tech reps based on runsheet column 'Source Name' instead of Sample Name "_techrep#" substring
commit 38a972f9641e41ab3bb06e88859ba746338bbc20
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed May 28 21:43:24 2025 -0700
Update listed project scientist
commit 1aaee9f112300555e83956b82b93b11eb0821ccb
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 23 18:06:52 2025 -0700
- Do not collapse reads for datasets where only 1 techrep was kept for relevant samples; update stats group assignment line
commit 4bc0dc5f79de69c581524f2cbdf437c8ae0b786c
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu May 22 18:17:50 2025 -0700
Update resource allocation for ADD_GENE_ANNOTATION processes (#155)
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
commit 8c7835cb5f5d11e5e8a12b1d1908b556da95f744
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed May 21 18:51:38 2025 -0700
Update nextflow.config
Set validation mode to lenient to allow number input for input parameters with string type (for example "--genome_version 112")
commit 3216f87f1e3cc11ff886851e7009cf6bd4830033
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed May 21 18:13:53 2025 -0700
- Add runsheet publishing to GENERATE_PROTOCOL, this is redundant for the main workflow, but will add runsheet publishing for `--runsheet_path` workflow runs
- Allow POST_PROCESSING:UPDATE_ASSAY_TABLE to succeed with no output in runs where no ISA.zip was used, for `--runsheet_path` workflow runs
commit 7c21454a28032764ecf3e8824fea2fc86f780e63
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed May 21 00:48:48 2025 -0700
Custom organisms patch
commit 280eaed497e99c4d4a0fb4b9268f69b965e3c399
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 20 21:21:29 2025 -0700
Add VST try-catch to microbes doc
commit 942c23aea13eb00d7ae2661ea8573e4e8435039c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 20 21:05:28 2025 -0700
reduce index building memory allocation, remove cpu * task attempt specification
commit fccdd0771cec5b3d3cc625a5b11b20cb969102e3
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 20 18:39:03 2025 -0700
Add try-catch for vst failure: call varianceStabilizingTransformation directly
commit 908d33834bb843353723b64b35e95426dfe0df71
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Tue May 20 18:46:48 2025 -0700
Update update_assay_table.py
remove "R1" from single-end unmapped.fastq.gz suffix
commit 921d40e51734a9248ac9344e7dd9a98b6c5ddcd4
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Tue May 20 18:00:37 2025 -0700
Update align_star.nf
fixed underscore typo
commit e2a7ff28bc423f745a590ed84c1e2a2673a197d0
Merge: d5dc4ed d178627
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Tue May 20 13:00:12 2025 -0700
Merge pull request #148 from torres-alexis/null_annotations_bug_fix
Misc fixes
commit d178627f76397ab6b1b5695d1803f2458251c35d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 16 16:41:35 2025 -0700
Allow integer sample names - finished
commit 8a2a38a5c868a5285e5b76c1de8af0b3c678e075
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 16 14:43:47 2025 -0700
Allow integer sample names in input runsheet
commit 89a4039ca8fd3556e346c3158cf2f2310a81a2a8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 16 12:56:25 2025 -0700
remove unused sort_into_subdirectories_by_sample.py
commit 367ca56723743e440782a86ec4b4c770a9c035e2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 15 16:21:00 2025 -0700
finish SE unmapped reads name fixes
commit c1e6603275341b2910642c1461ea8c43564e1468
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 15 15:10:41 2025 -0700
Remove _R1 suffix from unmapped SE read filename
commit f69a322861bd808df3b916158be1bf18973908a1
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 15 09:20:01 2025 -0700
add generate_md5sums to config
commit 043d1919de95d9540ac15401ba59a9bbd470253a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 13 11:54:14 2025 -0700
make local.config match slurm.config
commit c8f2bcc9170ebefb3dd06862d32935434d8f5c40
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 13 11:14:43 2025 -0700
- ALIGN_STAR: finalize genomeLoad setting for use with 2-pass
- Rename and gzip unmapped fastq outputs
commit 84acd74ff8cd59f5dda5890874c75b22774699ec
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon May 12 18:04:12 2025 -0700
move parse annotations table to modules
commit 84eeaa17c2e9a0f9e237801fe6276321d125ce29
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon May 12 17:27:48 2025 -0700
convert parse_annotations_table module to a subworkflow
commit 3c278a3525150c7cc2f857f5a04220d3055a2fc8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon May 12 12:21:59 2025 -0700
Change parse_annotations_table to script block
commit aac1d523df2a8eda3542262737ac6c2cc0919c77
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon May 12 12:04:20 2025 -0700
Move parse annotations table color defs to exec block
commit a963cc5fb76cddd3186a68f9461038293efdaf5b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri May 9 00:32:34 2025 -0700
increase align star mem
commit 6d07013c9651853eaabb20070514e8dbe57b3ab9
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 8 23:36:16 2025 -0700
update changelog
commit eecf3b6d8f0f8406f4d64e89f3759e54a5c57ade
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 8 23:13:27 2025 -0700
vv dge - explicitly set sample names as string
commit c0e044eb12f1f6c24aec67c583d480e4b20bfd95
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 8 13:26:47 2025 -0700
RNAseq slurm - increase submitRateLimit
commit 094bc735f7790342fd98d92d6ca3334fe542bf14
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu May 8 11:59:38 2025 -0700
RNAseq - update resource allocations
commit 296943b32dfd84f5f754cdc5eba6ce2d659af12e
Merge: 7dfbb47 eee1c4c
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu May 8 10:38:14 2025 -0700
Merge pull request #152 from nasa/DEV_Metagenomics_Illumina_NF_conversion
Metagenomics Illumina NF conversion and pipeline update
Pipeline updates:
- Update tool versions
- FastQC
- MultiQC
- bowtie2
- samtools
- CAT
- GTDB-Tk
- HUMAnN
- MetaPhlAn
- In step 14d, MAG taxonomic classification, added the new --skip_ani_screen argument to gtdbtk classify_wf to continue classifying genomes as in previous versions of GTDB-Tk, using mash and skani.
Workflow updates:
- Update to the latest pipeline version (GL-DPPD-7101-A)
- Implement workflow in Nextflow (NF_MGIllumina) rather than Snakemake as in previous workflow versions.
- Run checkm separately on each bin and combine results to improve performance
Workflow Bug fixes:
- Allow explicit specification of the humann3 database location [Metagenomics Illumina] explicitly setting humann3 reference db locations in rule, fixes issue #62
- Package bin and MAGs fasta files into per sample zip archives [Metagenomics Illumina] Some datasets have too many files in the MAGs and bins folders, fixes issue #76
commit eee1c4c2e7b78a759623e0adba3b130765d1b588
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu May 8 10:23:37 2025 -0700
revert permissions on SW_MGIllumina scripts
commit 55f66a2cedbc550f5cf1fe1ed11b182a5d4754f0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed May 7 20:47:04 2025 -0700
Update build_star_index limitGenomeGenerateRam allocation
commit f9dec7c3eae8583461873e3e203cea6be8508c30
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Wed May 7 17:03:06 2025 -0700
[DEV_Metagenomics_Illumina] Minor documentation updates (#151)
- Pipeline doc
- fixed typo in sed command
- NF workflow doc
- added explicit definitions for all profiles available
- removed slurm from example command-line calls
- updated headings to adjust slurm removal
- simplified instructions for different run approaches
- added conda env configuration information as additional information under the conda profile definition.
commit d71970c9f179fe9a1d6ac05ea027725985c4c755
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed May 7 12:38:49 2025 -0700
Add slurm executor settings
commit 7986bba2e0eb3d350f9533e200158e3ef334e9ea
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 6 15:36:54 2025 -0700
RNAseq: reduce resource allocations
commit 4d086192043a91dec7ba0dde335a8d16cbd1c011
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 6 14:07:05 2025 -0700
change genomeload from loadandkeep to loadandremove
commit d7c3cc0b325bc4e4e3a0fbf21dfe09ad6c7d14ba
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 6 13:48:41 2025 -0700
move new align_star parameter above read Ins
commit 30730e3feafdd1684c69b62aa3e43a0f6aed1725
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue May 6 13:45:50 2025 -0700
STAR alignment: add --genomeLoad LoadAndKeep
commit f8846996ba695e2043cfecf28a884e35ab09f101
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon May 5 10:05:42 2025 -0700
vv bowtie2 alignment - account for empty unmapped fastq
commit 2a16111b08bf6edb6c86211e3cbc0426d0cea1af
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Fri May 2 17:03:50 2025 -0700
Updated documentation (#150)
- Updated Pipeline doc
- added missing output files for assembly based processing
- added links between steps for file references
- fixed step references
- Created examples/runsheet folder for CSV examples files
- Added runsheet documentation
- Updated ChangeLog
- added ChangeLog documentation
- reformatted references to pipeline and previous snakemake workflow
- added closed issue references
- added other workflow specific updates vs previous snakemake
workflow (checkm implementation)
- Updated Workflow README
- add docker references since both Docker and Singularity are
supported
- regularize capitalization of Nextflow and Singularity to match
the tools' documentation
- reorganize post-processing output definition to match other assays
- clarify installation instructions for conda in workflow document
- Added missing assay suffix to "Failed" assembly file name
- Rename NF_MGIllumina-A to NF_MGIllumina
- Checked and updated all broken links
commit 620598fc0e4df529579b5ea1b4d333066bd10dab
Author: OLABIYI ADEREMI OBAYOMI <obadbotanist@yahoo.com>
Date: Thu May 1 15:14:55 2025 -0500
Metagenomics Illumina Nextflow conversion (#134)
* improved checkm performance by running separately on every bin
* fixed typo in config
* updated the nextflow version
* changed the default value of accession input parameter
* reverted AmpIllumina pipeline doc to remove updates
* added launchDir variable
* made format changes to config files
* updated README
* updated MGIllumina pipeline doc after CCB approval
* added launch scripts and fixed bugs
* deleted cluster path
* fixed humman utilities mounting bug
* commented out singularity cache_dir
* updated the content of processing_info.zip to match other GeneLab Nextflow workflows
commit 747505a5e590e3398e00ee67a13d46bc6bcad28d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Apr 29 18:14:14 2025 -0700
add tech reps line, fix syntax in ending, in generated protocol
commit dfbd39d4f70a66f77915ee63cc9f370f5c0619da
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Apr 29 17:27:52 2025 -0700
generate protocol update
commit 7d04121babc9a6658dcf9cc2f7675115b489ae5d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Apr 29 16:58:00 2025 -0700
add wf version to software table; update assay table patch for protocol col, raw multiqc in-place value fix
commit 98b49a615b760d603813b9b3e6d805e4a8cf4557
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Apr 29 13:10:29 2025 -0700
fix broken file path for vv rsem multiqc check
commit 607c324dcdb0dd173c85bb15a8e6f578833f98e2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Apr 25 14:50:50 2025 -0700
clarify log2fc vv dge log entry
commit 709916da34ec05b7d2aecffaad08cb9b3d324f2f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Apr 25 14:27:08 2025 -0700
fix null annotations error
commit d5dc4ed8f40a4d4b82f21ecd1d414ff221fd64df
Author: alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Fri Apr 25 10:52:32 2025 -0700
undo pending assay table changes, add suspect log2fc table output to vv dge (#147)
commit 325031db2494f9892074a02e9ee52c69031730a2
Author: alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Fri Apr 25 08:49:03 2025 -0700
remove extra } in rsem index storeDir path (#146)
commit cf3450baa2584498670b66fee38978308b97979b
Author: alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Thu Apr 24 19:21:44 2025 -0700
[NF_RCP] Miscellaneous fixes for NF_RCP 2.0.0 (#144)
* fix typos/bugs
* fix vst norm counts file name
* fix prokaryotes pipeline image
* set align_star to 8 cpu default
* add org version to protocol
* [NF_RCP] Prokaryotes - update unmapped reads se/pe output in docs
* Add docker notes
post-processing:
* update assay table updates
* add raw multiqc col, remove non existent STAR rrnaRM file
* fix duplicate col issue in update assay table
* publish rrnarm counts
* add rrnarm counts to assay table
* change unmapped reads col name
* fix pending columns
* update assay table typo fix - featurecounts multiqc
V&V:
* feed trimming reports into trimmed reads multiqc, update vv
* finish reads vv updates
* fix adapter content check in vv
* fix vv rsem script
* fix vv dge log2fc check
Output organization:
* update docs to reflect trimmed multiqc update
* fix dge script - account for rrnarma changes
* add fixes for RNAseq outputs
* chmod +x script
* remove rrnarm specific output folders, move duplicate sample table and contrasts table
* move raw and trimmed multiqcs to dedicated folder
* move alignment multiqc reports to dedicated folder
* move counts multiqc reports to dedicated output folder
* move rseqc multiqcs to dedicated folder
* fix typo on trimmed data sequence / fastq
* add md5sum file filters
commit 7dfbb47774bba3e61179f17c3a2e58429787fb23
Merge: d81c2c0 e6fb470
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Fri Apr 18 00:25:08 2025 -0700
Merge pull request #145 from nasa/GL-DPPD-7113-patch-1
Fixed treatment vector to always assign "treatment" state to 1st group in contrasts vector and "control" state to 2nd group.
commit e6fb470af8f90be4fe71ccbd6989aa9a72b0b4ac
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Apr 17 09:34:25 2025 -0700
Update GL-DPPD-7113.md
Fixed treatment vector to always assign "treatment" state to 1st group in contrasts vector and "control" state to 2nd group.
commit f646141eceffaff54e1a3cf12f6530f8e7d8a249
Merge: f48e788 829828d
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Thu Apr 10 07:57:59 2025 -0700
Merge pull request #142 from torres-alexis/DEV_RNAseq_vG_pr
Updated Eukaryotic Pipeline to GL-DPPD-7101-G added Prokaryotic Pipeline, GL-DPPD-7115, Updated Workflow to [NF_RCP] 2.0.0
commit 829828d5e89d1b14873d6b88ab3ee44a2bb817da
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Apr 10 07:45:04 2025 -0700
Update 2.0.0 date
commit 7a4066796c446c3a27e24410cefad372d908c67c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Apr 10 07:35:53 2025 -0700
update changelog
commit ebc07cd6214d1c05f29c99eac26fb02044fa28bd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Apr 10 07:16:11 2025 -0700
fix typo
commit b7bd50a6f6765b302eeff1552940404475b580f5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Apr 9 20:37:43 2025 -0700
[RNA-Seq] DGE: Unfilter tech reps from unnorm counts
commit d81c2c0c260d841cea8b370bef655862022b2138
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Fri Apr 4 10:07:23 2025 -0700
Update GL-DPPD-7113.md
added dp_tools software to software table
commit eead37afcb9705346e97d7be0860b52577a66c43
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Apr 1 12:47:28 2025 -0700
add nfrcp readme revisions
commit 6b22f44078c250143142a06fd3364e7f2692e91a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 28 12:17:10 2025 -0700
Display flowcharts
commit 6fb57508794d3f3d66c9436cde5ce52ca47dc318
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 28 12:02:51 2025 -0700
update images
commit a0635dbff1e6890266130e00056de52d985991a6
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 28 11:57:19 2025 -0700
point metro map image to png
commit 17d94930ad2733349eb0f838b2b0aff1d2f4b133
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 28 11:56:39 2025 -0700
update image to metro map
commit ca470dec144709f90abae7d5667fe7704db1dbb0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 28 11:55:18 2025 -0700
update link to pipeline pngs, add metro maps
commit 5b942ce07bd7860895be41077b05dfac214c0faa
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 23:44:31 2025 -0700
add read count col to update assay table
commit 35fdd28d5578260cdb6c8b7345a223bf84d4aaa0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 18:37:58 2025 -0700
update images
commit f8200cb3f9ce3659524abd7cf0d13214928fbfbc
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 16:09:05 2025 -0700
add metro map files
commit 03b6b16a9db670901fd5cc256ec48c131d5f2368
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 15:00:35 2025 -0700
add drawio images, update text
commit 9cae0fa7522499493cacf85e5317023bfbdf5859
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 13:23:12 2025 -0700
add processing_info_GLbulkRNAseq.zip
commit 09274180fb43474839ec6b49680c1cbc1cf60a56
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 12:29:48 2025 -0700
update pipeline images, make tentative updates to readme
commit f61a43d2ea1f07bc9a40748692789c17cf41a2db
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 11:52:38 2025 -0700
readd NF_RCP-F folder, readd envs subfolder, update docs reference to this folder
commit 2176cf40b402f28b203106a84f51992946f88bae
Merge: 4a6ef36 ef2b9f1
Author: alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Thu Mar 27 11:39:13 2025 -0700
Merge branch 'nasa:master' into DEV_RNAseq_vG_pr
commit 4a6ef36e6c00cf634825f94ff226012a9e174c68
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 27 09:58:15 2025 -0700
increase genebody coverage mem
commit 17b6f271354be260d796583083e62f9ff6113095
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 26 22:45:06 2025 -0700
fix typo
commit c706a384da9cb074301075c12844e50ee9fd457f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 26 21:57:40 2025 -0700
fix typo
commit 91c99f717e2d8c698b82f0815798bc97a2b1fddf
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 26 21:50:38 2025 -0700
add updates to nf rcp read me
commit 5b38f646853f56f5020c41d866d11e61d7fe2841
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 26 21:49:48 2025 -0700
add vv updates
commit 66fa468a1dc372cdd960937f21ffb8744c478d6a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 26 14:03:22 2025 -0700
update microbes vv scripts to include flag code
commit e16bae040a89ae03560be6f2aed1cf7d19a46538
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 25 13:17:45 2025 -0700
change nextflow_logs to nextflow_info
commit fa819d11e20a6f8d221e2f3360470e413d061dcd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 25 12:58:22 2025 -0700
fix typo
commit f48e78892e394df0c81af075f04eeced84c59b7c
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Mon Mar 24 09:49:37 2025 -0700
Updating submitter
commit bd43c64e3fae52664b1a7cf59b19e967d6e9381d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 22 12:39:08 2025 -0700
skip sam_to_bam in workflow code; leave in docs
commit 829093c313c88e6a67b4f085e1e6546a6b50eeeb
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 22 11:23:15 2025 -0700
add combined bowtie2 and samtools image
commit 8d736ae3284b0f75d7f5b3113260275803d8aba7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 22 00:52:30 2025 -0700
update pipeline docs to reflect multiqc output changes
commit 119b6be49e5150f89a03a5a7b411ba4d50988595
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 22:02:19 2025 -0700
fix isa input
commit e4c4def97f4b7d5062a61362ebf784fcb8e633a0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 21:54:43 2025 -0700
fix typo, unhide limit_samples_to
commit 075abd64fb822755468b59661217ee25fa488093
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 21:50:14 2025 -0700
add publishing to STAGE_ONLY entry
commit 2f0166df389c570b59faa760c6b38065c9e840ee
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 21:21:40 2025 -0700
readd stage_analysis
commit 9c5f0c3e573640a4cbd4207910ace5b3a630cbd2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 19:25:42 2025 -0700
clean up workflow code, readd all_multiqc
commit 5c0c777e4c23ad1fb99b27e5f923c494e222d58b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 17:48:47 2025 -0700
make parse_qc_metrics work with runsheet run
commit b714ff659c055946b991fef20cc00045cbd34e1a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 16:49:44 2025 -0700
add runsheet truncation (not published) functionality
commit a3d5aacc6f59b0c4c44f5108d0dc96a559f5226f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 21 16:38:29 2025 -0700
move dp tools reporting to vv, fix runsheet truncation
commit fa7054c393df2c6df2d6ae27c86f54d72d8fde34
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 20 21:19:06 2025 -0700
fix vv log
commit 97225fc78c23b634221bc1da721afaa55ea748bb
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 20 21:10:45 2025 -0700
manual fixes for missing software versions
commit 60d6ff6aad743e545f3e659f5a1bba2631fc010e
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 20 20:39:40 2025 -0700
Make r scripts executable
commit 8402693ccaf1e22693433deb3c824838db780db0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 20 18:45:07 2025 -0700
fix typo
commit ac46059ca686bed80a8e30c29815fb26de748b9e
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 20 14:18:32 2025 -0700
clean multiqc paths in multiqc process
commit 7c4a713e78002bda234182a26f0a47a067436ade
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 22:07:01 2025 -0700
update featurecounts nonzerogenes script name
commit 88243519c3ab6c489ca2766f7845e6aa20c89e23
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 19:31:19 2025 -0700
update_assay_table changes for multiqc outputs
commit 436887c65802b744a955dcb69ef6ca9cbeb0be49
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 18:40:17 2025 -0700
typo fix
commit 2d9caff3ebbda2186bb259dc107601d5e92591cc
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 17:22:17 2025 -0700
fix typo
commit cf305aa789f735b0fabea30ce52d3a237a91e2ae
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 17:16:29 2025 -0700
remove dge rmd paths from nextflow log
commit 90324e5cc66ef26207a08870d73519a15b256bd9
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 16:43:47 2025 -0700
update multiqc outputs in vv scripts, add featurecounts numnonzero
commit 9cd6c1c09cc08e312ff5bdab13dad60e01e699b6
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 14:40:41 2025 -0700
hide broken debug param
commit 3bbeb46faee9b92f11e0b0997c7cdf791248209a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 14:08:58 2025 -0700
update schema
commit b036a4605365b2eea23c4d5ba283233bbe0c16a5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 19 13:35:46 2025 -0700
change multiqc output format, set up vv module
commit abec98e2e4264bdb75c27b8693c0327edb968142
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 21:36:26 2025 -0700
disable conda in docker profile
commit d64416229e135202c731e6d41ea045557e6d181b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 21:34:16 2025 -0700
remove log validate params, update manifest, version text
commit 1ab31e279443c99f4ae93df98cfa5339cd3cbb4d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 21:08:39 2025 -0700
fix typos
commit 9a87a5d7457e5a2e9aa3c7516277165a0c2ec93c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 21:00:02 2025 -0700
update fetch_isa to use OSDR biological data API
commit 2f020b50149839c40d08665f5c9b961630bf7619
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 20:44:18 2025 -0700
OSDR bio data api update for get_accessions
commit 31e1600202c3863a6406ee215fc849f0bf990c4e
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 11:27:23 2025 -0700
Add download_references stub in line with custom ref inputs
commit c063c218b92681e94aa33bc4af44471c00d10a93
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 18 11:25:57 2025 -0700
allow for files in annotation table, fix gtf to bed path
commit 593dd71223db003e6fd9a91f796e7166e6712188
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 17 21:39:41 2025 -0700
update extract_rrna
commit 400c156092f24681da25877dc85b19d4df76ba68
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 17 21:22:37 2025 -0700
add updated ncbi gtf to bed script
commit 5657f7b4dac5c106cdf529f3219f98783582970f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 17 14:32:55 2025 -0700
misc fixes
commit dcdd529e445bbefdca214c9acb1f7c3c86b93164
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 16 20:54:17 2025 -0700
account for ncbi gtf groups, allow infer expt fail
commit e41298cf6533f19daee0c370b536d58d2455eb05
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 16 17:13:02 2025 -0700
readd gtf to bed
commit 375bb64acc16ca4c701a3a25f5f566d071a01bed
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 16 11:30:26 2025 -0700
finish update assay table fixes, make scripts executable
commit 650c7e6df8d6859b2cf10ed3feca488af4d556c7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 15 23:34:53 2025 -0700
fix update assay table, misc vv fixes
commit f097e345d9cf5d790b56a03e997b071e79ec5b36
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 15 22:06:57 2025 -0700
remove vv stats file output
commit 5c421e47dcef3a11926621cdea76422891974126
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 15 15:46:02 2025 -0700
add vv_rsem, add vv_star stub, define vv checks
commit 23d5c968bd9f46cb935f10b9e56652d8b6b7faae
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 14 23:50:57 2025 -0700
vv dge fixes
commit a3735248e790d73cc47e868d9d543c048e61b34d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 14 20:34:37 2025 -0700
fix dge tech reps filtering for rsem
commit 2c668b96f0d6df71b5a65539ada27cf1fbaef6f5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 14 17:33:41 2025 -0700
add generate protocol to rnaseq workflow
commit 449981da5ecbe4b950e6996e86ae5cdc6f83471c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 14 16:20:20 2025 -0700
fix version reporting
commit b48c7c2e283b1e95bda31ab4c3e72fc07d495c8f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 14 14:47:28 2025 -0700
set up vv publishing draft
commit 161c2ccf1821c1c323fa96e5d75ce6f7ed248630
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 13 16:52:28 2025 -0700
rnaseq misc fixes
commit fb09cb7745dca58ec13edef39361e90d9b4a0ea3
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 11 20:27:36 2025 -0700
update python envs
commit 137d5615a643d58470a5eecb3d40d1953b941575
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 11 19:33:49 2025 -0700
fix update assay table
commit 5f9ccc9df726c9e2167345d6c6a31bab358f97e1
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 11 18:47:15 2025 -0700
Remove comma space separators from assay table
commit 56d42b276141a46c8783f81aa12dfb2eaeb87ec2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 11 18:13:51 2025 -0700
Update nextflow version
commit 4fbae882eac5c935cdb0682dccfb9edb0e506556
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 11 12:18:33 2025 -0700
add generate protocol to microbes workflow
commit ad80b55bb81d2786eff38f4c1590f3c956d391a3
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 22:18:36 2025 -0700
finish update assay table for microbes
commit 98b4e6d9f95b880c75032203f0d473f0721b2aef
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 22:18:16 2025 -0700
publish software table
commit 654c11206ec6b5f471663879343e60ff9edcb6d8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 20:54:43 2025 -0700
add update assay table stub
commit 649d20bfbef68c9dd9b2acfeade41244ecbcad87
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 18:10:41 2025 -0700
add generate_md5sums
commit 272c45f703170f79df2b1fe8fcf9013e38ec41e4
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 14:58:04 2025 -0700
set up for md5sums
commit 7fca3705b6c66c681bb4919154ec3159a91e2a0c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 10 13:43:36 2025 -0700
vv dge, minor adjustments to other vv scripts, remove vv.py
commit 8ccb9a5a522cf41a132eb96ae13a6e62e9944460
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sat Mar 8 17:10:48 2025 -0800
add param updates to featurecounts
commit 31aa3cff10324d2f3fafdbd8dc5fa0c9456f4daa
Merge: 866ebd5 462c2ab
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 7 17:40:59 2025 -0800
Merge bowtie2 and featurecounts updates from nasa/DEV_RNAseq_vG into devevelopment branch
commit 462c2abf29b9269da9540c2efe2cf04a1fe4f51a
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Fri Mar 7 14:08:29 2025 -0800
Updating options based on AWG feedback
commit 866ebd5ab13d7cbef3742a41e8524d45b04874d8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Mar 7 00:06:01 2025 -0800
Update DGE script to clean up group names in DGE table Group.Mean and Group.Stdev cols. They should now match the expected format from GL-DPPD-7101-F
commit 5d0859ef3a0a24cd2bd0c3cc33f4d39f504011c6
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 6 19:19:07 2025 -0800
Remove -G from RNAseq/Workflow_Documentation workflow versions
commit 88a153de201fa94d55557755e8e2cb6943fdab02
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 6 18:51:50 2025 -0800
Clean up sample names in featurecounts output
commit af171edb75babd4b011df9997b007addfc1b8956
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 6 18:09:42 2025 -0800
clarify bowtie2 -a definition
commit f5ed5caac5be268b5fcdd9349819c56126990060
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 6 17:47:18 2025 -0800
Add -a to bowtie2 alignment and --primary to featurecounts
commit 3360942a8942f91f162bbf40b87556b38a843d67
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Mar 6 16:48:53 2025 -0800
Set default BiocParallelParam to SerialParam()
commit 9edfadaeed3be46346c2b495d0bda113001cb945
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 21:07:59 2025 -0800
add vv rseqc script, rrnarm label
commit 7a68291d2521c4f261721422d78b5d144f948682
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 16:24:39 2025 -0800
Add rseqc / R container, set up vv dge stub
commit e5c51935b429d3a31e6d03718ccbb184e6bc6a05
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 15:59:43 2025 -0800
Add rRNArm label to DGE outputs; set up VV DGE stub
commit 392f78228e97f26325e3b620f0ab38e73b9472d5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 15:15:04 2025 -0800
fix typo
commit a62f2e62ce0e01cab282f94f2cd58278b9ca579f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 15:14:03 2025 -0800
add vv featurecounts
commit 24a28926600726555bb093a41642545f0bb83877
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 12:48:38 2025 -0800
add vv rseqc stub
commit 43c7faf3de16c374a199e9dee8544894d26087a4
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 11:04:27 2025 -0800
wrap up bowtie2 vv
commit b32b5720c35c785fbaab5c728da6a5c08aa750fe
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 10:35:43 2025 -0800
Add up to bowtie file existence vv
commit f056d602642717771dc024dc9dd9c25e43c41356
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 09:57:25 2025 -0800
add vv bowtie2 stub
commit 3a655a1e277df7866d9011c79e199974a4009ff7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 09:56:36 2025 -0800
add vv trimmed reads script
commit 7665995e3d511a8845ec24e343f6ebba9ef0d239
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Mar 5 09:22:47 2025 -0800
finish vv trimmed reads standalone
commit b061496788b39b8161db29575de6932b4f879ce7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Mar 4 16:53:12 2025 -0800
set up raw reads standalone vv script
commit ef2b9f132e9945f6d5fd001c10c952ce34c4a44f
Merge: 810fc7a 53e8666
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Tue Mar 4 08:09:37 2025 -0800
Merge pull request #141 from nasa/DEV_Methylseq_250115
Update Methyl Seq pipeline as follows:
Added a filtering and normalization step prior to differential methylation analysis. For studies in which the coverage is fairly similar across the samples, this step will not change the results, but in the case of outliers it will improve the data quality. See Step 11e for the complete implementation details, in brief:
Normalize the data
First, filter samples by coverage to account for PCR bias or over-amplification
meth_obj <- filterByCoverage(meth_obj, lo.count = 10, lo.perc = NULL, hi.count = NULL, hi.perc = 99.9)
Normalize coverage between samples using a scaling factor derived from the median coverage distributions
norm_meth_obj <- normalizeCoverage(meth_obj, method = "median")
Combined all pair-wise differential methylation analyses into one output table for bases and one output table for tiles, rather than providing individual sets of files for each comparison and splitting between hypo and hyper methylated regions.
Provided the differential methylation output without filtering, rather than imposing significance cutoffs.
The new output format matches the output formats we provide for our other assay types.
commit 53e8666d7d73b326ae871a71e711cfa6f6e5c4b0
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Tue Mar 4 08:03:21 2025 -0800
Updating approval date
commit f84d22dea15c81e0fa634a4cca9f91a64c98b4c5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 3 15:27:38 2025 -0800
Add vv featurecounts and fix publishing, fix rrnarm featurecounts name
commit e96d20fa7e03e29a36bad542e08ef40caf542659
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 3 13:11:34 2025 -0800
update parse qc metrics for bowtie2 and featurecounts
commit a76e62456420af858f6befbe4d5faa32b582c717
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 3 00:07:50 2025 -0800
fix vv pe setting
commit 6e3476f7039162aa74c32f6a325cb5f4c6f3a9db
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Mar 3 00:01:09 2025 -0800
add up to rseqc PE
commit 1ebbcbb320d88e6c6bba86491e23a0c47afc52f7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 2 22:57:44 2025 -0800
finish vv bowtie2
commit 21cb173cf79aea6576f48f3fa5a25e6c73c97ab7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 2 22:41:47 2025 -0800
add bowtie2 to parse multiqc
commit 92a1189885c07f6222876c832a16b88d56c2c7ac
Author: Alexis Torres <lextorres46@gmail.com>
Date: Sun Mar 2 22:11:58 2025 -0800
finish trimmed reads vv
commit 01018cbede2a6d4f6e6dd6aadcfffb264992a852
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 27 21:21:51 2025 -0800
add parse multiqc stub
commit a4cde560cd3c8da36fbc5a442f7880901c0ee154
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 27 21:21:19 2025 -0800
add qc metrics stub
commit 7abbf98a588e883be062321407098c769a544078
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 25 21:40:13 2025 -0800
fix vv log publishing names
commit 2fc2683b8fbf0b70176f445fdefb36aa8ebc1184
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 25 21:32:51 2025 -0800
add vv rseqc
commit 6854fba90969cca43fd270ac789b020bcb5a4af2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 25 21:32:20 2025 -0800
make rseqc output filenames consistent
commit 6edc67fcb73c35c4c5d5168845166ade8d17fa90
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 25 17:19:33 2025 -0800
readd --force-single-end
commit 8d22bd072bb203d3bf9222c9ea4136d3e3cea1d7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 25 16:42:49 2025 -0800
vv bowtie alignment
commit ae81c453b08ab2d071ec7261cf658687297e4033
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 22:45:20 2025 -0800
add vv trimmed reads
commit 5bca9cef3356ac5d68720bf3667ac83c89051402
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 20:16:13 2025 -0800
make multiqc module label more flexible
commit 484d17300d14470aadb4f0a110a5ded57fda0a52
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 20:00:35 2025 -0800
set up dge step to take in rrnarm counts, prefix
commit d6427e82040e11d969c87c5ba1c3f1571b3c6691
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 19:59:39 2025 -0800
finish multiqc path cleaning draft
commit c773c396efa7f4a780d6a62325f56ecd6b3a7514
Merge: dd68d0c 2f444cf
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Mon Feb 24 11:59:45 2025 -0800
Merge pull request #139 from torres-alexis/DEV_RNAseq_vG_CURRENT
RNAseq Updates
commit 2f444cfa110946e4d8ad4c537a0c9e8f54d8395c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 11:56:43 2025 -0800
Add stub for multiqc path cleaning
commit cb6ade12525948b124d51ebbc18754fc13b443fe
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 24 08:39:16 2025 -0800
vv raw reads
commit c789d48eb1945d7c44c8979a4db932deed6cf16f
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 20:20:50 2025 -0800
fix typo
commit a6ae14e3adffdb67659d935453f994fdd83214f2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 17:29:50 2025 -0800
update docs
commit 4335c75e0080687aeea9bdb0b53d1dc670df34cd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 16:53:12 2025 -0800
update pipeline doc code
commit ad17a28d3cf7c5938ba78515c2035cbba7c8e9b5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 16:22:41 2025 -0800
typo fixes
commit c3baacccc7a73c1b6399df8ecf4c0b0246ee5403
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 16:21:27 2025 -0800
adjust dge group stats code
commit af90b65c93c835a9dc267c204e4d43c129f0277c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 15:35:02 2025 -0800
clean up dge code
commit a690b1dbe826abf34ff6a6b6d64e551021b34631
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 15:24:50 2025 -0800
clean up dge step
commit cc0cb5e02158c19cd74536f0f00b07fdcba5fe6a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 11:27:41 2025 -0800
add vv raw reads stub
commit 0561c64bba792c1e37d0f586a7c4039441e3769d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 21 11:11:10 2025 -0800
add vv raw reads stub, fix configs
commit ead77cb2ec33f612f3b4fc46ae7229482b986ccd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 20:06:49 2025 -0800
set up publishdir
commit 1ce81c3346f78bbd128c7590fb507cf868bb5fc7
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 15:50:22 2025 -0800
pass assay suffix into modules with params
commit bb856b5f882fdf7b46caf773a1c4a52d48562d3b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 15:40:29 2025 -0800
add assay suffix to md5sum module
commit e2b79c394964c292b8f6e3bf1ce28017a88f23eb
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 15:35:02 2025 -0800
clean up workflow code
commit ce6fdc1d7e61a14501f14224e2cc9174a10371cf
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 14:57:39 2025 -0800
set up output directory, improve workflow setup
commit 6623e2075bdd7b7c4bdefc7f67946296c2cf196f
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Feb 20 14:53:42 2025 -0800
Update GL-DPPD-7113.md
Updated Step 5 to include a zip command creating the final zipped output file for that step.
commit d190e673e7d31a89500c5c4a3dae142d1bdb4356
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 20 12:05:37 2025 -0800
clean up assay suffix uses, fix help menu
commit a8c7f5f664454b9b0a53b676b8c5fa2fee3cf86c
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 19 19:44:00 2025 -0800
update deseq2 image, nextflow version
commit 903f8a0d7dc1b18bbda2ed59b227d720034fe449
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 19 19:12:26 2025 -0800
Clean up (baseline) date
commit f591d5ffb5c1e6f5d39159c4bc9da787d7c7e38a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 19 19:08:36 2025 -0800
update readmes
commit 6471d7a620a4f0f5a26decc100fd7aa979599591
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 19 18:15:32 2025 -0800
clean up dge step
commit 7ecd205430b9aced9e87eaa5617499a598607aa6
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 19 13:56:37 2025 -0800
Clarify DGE code
commit e6aa9362c190a7ce159a0192edec36917498c9f6
Merge: 0388ec8 979ac1c
Author: Alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Wed Feb 19 10:23:10 2025 -0800
Merge pull request #23 from asaravia-butler/patch-3
Update GL-DPPD-7115.md
commit 979ac1c62255bed17ff9ceb6d8ecafd9b735be06
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Tue Feb 18 23:07:04 2025 -0800
Update GL-DPPD-7115.md
commit 0388ec8feff29ae86960d0daedef74aa507166d8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 18 18:48:19 2025 -0800
update for addParams deprecation
commit 6559480da0f700ab06c7f637551fca47a22f4cba
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 18 18:31:47 2025 -0800
add schema file check to runsheet read paths
commit a5b15a0782f41382206cb64b3070875e898a2c09
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 18 18:18:21 2025 -0800
add draft runsheet schema check
commit 91114a0d0774448c9a59bc917e8ae89feb2305c4
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 18 17:14:57 2025 -0800
add nextflow schema without runsheet schema
commit 72fe63edc3b993bab54458770e0dcdcb630ac289
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 18 12:54:19 2025 -0800
add md5sum functionality, to do: finish implementation
commit d3c0b893c80a91529cbf1405583c890db3ad6cc4
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 14 02:24:20 2025 -0800
fix subread version
commit b32a550ab95112d4362987b2830e6e2d632cf050
Author: Alexis Torres <lextorres46@gmail.com>
Date: Fri Feb 14 01:20:17 2025 -0800
Add software version reporting up to dge
commit 2c3d81a866b76f66fc6d7abd069399018562d8f1
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 23:47:21 2025 -0800
Add versions reporting up to counts
commit 76b5c7b76ed529634df7096b8e10d7f2a0c8186b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 23:23:30 2025 -0800
add software versions yaml
commit 1dae39d02a0d1477ae398f280a6ec0b1ce9b5f5b
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 22:46:43 2025 -0800
add paired end info to featurecounts params
commit 561f4ced7648baed12e936e39b36d833757f3f18
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 22:24:52 2025 -0800
Fix featurecounts file extension, add rrna rm
commit 917843100488add6c85de79088f882100630498d
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 19:48:35 2025 -0800
Add gtf features to featurecounts
commit 7c161a1fb9589c185e00b36f0374e773c68c17ff
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 19:24:50 2025 -0800
finish featurecounts
commit b15d0e2cce766e1e6ed07f2940f46762e5eeea99
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 18:48:32 2025 -0800
add featurecounts params
commit 3f732cbad7b6b5db6c29ce6fb9d7dd0a706fe92a
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 18:03:58 2025 -0800
add featurecounts gtf features -t
commit f8779edb084d40cd0cd60dd5a947311ce85c9d68
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 13:43:11 2025 -0800
add reference file to featurecounts
commit 1470840f53d2344350bc935fbae78f4dd1000a20
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 13:04:34 2025 -0800
Address issues
Step 3: - Add --seed to bowtie2-build
Step 4: Set --minins and --maxins to 10 and 1000 respectively
Step 7a:
- Add --countReadPairs for paired-end data
- Set -d and -D to 10 and 1000 respectively
- Set -d and -D when -p is used
commit 2a6ec422f4d84192c44b8f9e33999648a4d22763
Author: Barbara Novak <19824106+bnovak32@users.noreply.github.com>
Date: Thu Feb 13 12:40:40 2025 -0800
Update pipeline document (#136)
* updated pipeline document
- standardized bismark output naming in parameter/output definitions
- added missing parameter definitions for all positional arguments
- added note about GeneLab suffix difference for DNA and RNA methylation
- removed bold formatting from files that are not output (trimming
reports and gene-to-transcript map)
- trimming report data is included in trimming multiqc report
- gene-to-transcript map is part of reference generation and not study
specific
- renamed deduplicated sorted output, alignment and bismark multiqc report output
- reconfigured MethylKit section to conform with output able format for other pipelines
- Combined all pair-wise differential methylation analyses into one output table for
bases and one output table for tiles (without applying any significance cutoffs so data
from all regions are available), rather than providing multiple different files and only
providing differential methylation data for regions that meet significance cutoffs.
- added normalization step prior to differential methylation calculation
- replaced write.csv with data.table::fwrite for differential methylation output
tables for better write efficiency when these tables are large.
- reconfigure workflow_code folder
- added isa_to_runsheet plugins folder
- added runsheet spec
- add runsheet generation step
- add definition for dist.to.feature
- switch to using species instead of name column in annotations.csv
---------
Co-authored-by: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
commit 15f889769ea171f7573e574a74094c8de5599243
Merge: be8e5b7 e978eca
Author: Alexis <71944751+torres-alexis@users.noreply.github.com>
Date: Thu Feb 13 11:48:08 2025 -0800
Merge pull request #22 from asaravia-butler/patch-2
Update GL-DPPD-7115.md
commit e978ecac43f2a76f296211d81a16b08bceca58d0
Author: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>
Date: Thu Feb 13 09:14:03 2025 -0800
Update GL-DPPD-7115.md
commit be8e5b7e3326fc71067a42fb42b5e0a932bbabbd
Author: Alexis Torres <lextorres46@gmail.com>
Date: Thu Feb 13 00:41:53 2025 -0800
add software versions stub
commit 5d850cd4536bce2d088be6a98f838aca83d630cf
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 22:10:29 2025 -0800
fix dge microbes step
commit 7f7e3c4d1fca45f76f4d860dcacd6acd284dcaa5
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 20:26:41 2025 -0800
typo fix
commit 9dc691b7cff2a6e3a3931ab3e87c119de6ee04b0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 19:45:51 2025 -0800
microbes dge step
commit e47cc7e6bafcd131b7b538a19616a8f69e3dab07
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 14:29:29 2025 -0800
typo fixes
commit f8771d13317dcfd7e898b94e750c9d4a205b8ef8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 13:03:37 2025 -0800
fix RNAseq docs 9a osdr links
commit 8ab3e8d8d3040dc98ad9ea2fc3f8c9a830258837
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 12 12:26:20 2025 -0800
Remove unnecessary nf module tags, chmod +x assess_strandedness.py
commit 5ab68a86f1f030ffa38733699285cefdfb5df5a0
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 19:33:20 2025 -0800
remove bowtie 2 --no-unal
commit 7952fb87a9f152cd12c161ea9541494f8eb59c10
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 17:46:38 2025 -0800
remove bowtie2 new params
commit 859aa35b05817490dd5351b660f45d55473ecd71
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 17:23:57 2025 -0800
change ensembl col name
commit 1c2390a942bbbd3a8ae9cfa33f448b496cf91958
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 17:10:27 2025 -0800
bowtie 2 typos
commit ddf1fcb7033a13b01e346e91626fe43f7d123e52
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 17:00:01 2025 -0800
fix docs
commit 6625a7eb8fe71f4ccae91457b989f00dd2e8f2e8
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 16:36:39 2025 -0800
bold microbes unmapped reads
commit 3f37b20be639c370e1bffa9d32646e82b3242f55
Author: Alexis Torres <lextorres46@gmail.com>
Date: Mon Feb 10 16:08:12 2025 -0800
update rnaseq microbes docs
commit 936a719a732f0eb8aa7e7a47ae9fa0e21b7d2404
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 5 18:05:28 2025 -0800
fix versions
commit 3690af42334c8d74e27ca5e3b3d126f72b313292
Author: Alexis Torres <lextorres46@gmail.com>
Date: Wed Feb 5 17:52:37 2025 -0800
add prokaryotes pipeline doc draft
commit ed57d45497cfbafe0d8ee6efe73663c5fe6533d2
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 4 14:39:53 2025 -0800
fix gtf to bed
commit 6d13c9234d895ea76e17473b5be04aace1d19b40
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 4 12:59:08 2025 -0800
add microbes partial doc
commit 1071eca9c83cf3c98a3c87482cdc300f27b56292
Author: Alexis Torres <lextorres46@gmail.com>
Date: Tue Feb 4 11:36:39 2025 -0800
RNAseq (Prokaryotes)
- 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
commit dd68d0c42b4dc24c320…
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Bulk RNASeq Pipeline updates:
Workflow updates: