Releases · bacterial-genomics/wf-paired-end-illumina-assembly

20 Nov 17:03

chrisgulvik

v3.0.0

12f5e59

v3.0.0 Latest

Latest

What's Changed

Round memory down for SPAdes by @gregorysprenger in #88
Add SKESA parameters to main params.config by @gregorysprenger in #90
Refactor profiles for use in Seqera Tower and add tower yaml for reports by @slsevilla in #92
Dev store downsample data by @chrisgulvik in #94
Dev to main by @chrisgulvik in #96

New Contributors

@slsevilla made their first contribution in #92

`Added`

Consistent metrics reported for each read cleaning step (@chrisgulvik)
Added SeqFu for FastQ format validation (@chrisgulvik)
Checksum (SHA-512) reporting of intermediate and output files (@chrisgulvik)
Report full input paths for each sample (@chrisgulvik)
For assembly depth reporting, added stdev depth metrics; added total paired+single mapped stats (@chrisgulvik)

`Changed`

Default uses SeqKit rather than SeqTk for downsampling (@chrisgulvik)
Output structure and filenames revised (@chrisgulvik)
For MLST, exclude all MLST databases with a *_ by default (> 1) to ensure the original MLST database version is used for each taxon (e.g., excludes leptospira_2 and leptospira_3) and avoids inconsistent versions used within a run which would occasionally give one sample a leptospira and a different sample leptospira_3 making it impossible to immediately compare between samples. (@chrisgulvik)
For MLST, store novel FastA when that situation occurs (@chrisgulvik)
Sample name in outputs and file content no longer contains assembler name (@chrisgulvik)
Changed RDP output to exclude unneccesary data columns such as "Phylum\nphylum", "Genus\ngenus" (@chrisgulvik)
Use both R1 and R2 and only Phred30 for estimate bp input for more accurate estimation of genome size (@chrisgulvik)
Changed default to always on to store stats and FastA of discarded contigs during biopython filtering (@chrisgulvik)
Output filenames within pipeline_info/ changed to show month by name and include day of the week (@chrisgulvik)

`Fixed`

Order of operations in Trimmomatic process now ensures final output reads have minimum sequence length (default: 50 bp) (@chrisgulvik)
Fixed issue with missing column header names in the .kraken_summary.tsv output files (@chrisgulvik)
Fixed trailing tab character in Kraken1 and Kraken2 output TSV summaries, which made pandas XLSX conversion fail due to different column numbers in header and data (@chrisgulvik)
Fixed VERSION reporting RDP bug by removing spaces (@chrisgulvik)

`Updated`

Coloring of workflow process now corresponds to tab color in XLSX output summary sheet (@chrisgulvik)
Docker container version updates (@chrisgulvik)
Updated description on output files based on new files created as well as some renamed output files (@chrisgulvik)

`Deprecated`

Removed gene calling from QUAST output summary (@chrisgulvik)

Full Changelog: v2.3.0...v3.0.0

Contributors

chrisgulvik, slsevilla, and gregorysprenger

Assets 2

21 Mar 01:41

chrisgulvik

v2.3.0

2e1c70f

v2.3.0

What's Changed

Dev subworkflow assembly assessments by @chrisgulvik in #82
Dev fastp by @chrisgulvik in #83
v2.3.0 dev into main by @chrisgulvik in #86

Full Changelog: v2.2.1...v2.3.0

Contributors

chrisgulvik

Assets 2

21 Feb 21:59

chrisgulvik

v2.2.1

b93a186

v2.2.1

What's Changed

Update path to Kraken1 database by @gregorysprenger in #71
Replace baseDir with projectDir due to deprecation in latest version of nextflow by @gregorysprenger in #69
Check if input FastQ files are corrupted by @gregorysprenger in #73
Patch: Updates to fix some minor issues by @gregorysprenger in #74
Set max resources for github action by @gregorysprenger in #77
bump to v2.2.1 by @chrisgulvik in #76

Full Changelog: v2.2.0...v2.2.1

Contributors

chrisgulvik and gregorysprenger

Assets 2

14 Feb 20:19

chrisgulvik

v2.2.0

50d1c5a

v2.2.0

What's Changed

Update documentation and other smaller updates by @gregorysprenger in #36
Allow user specified scheme for MLST by @gregorysprenger in #37
Rdp module by @taylorpaisie in #47
Update image themes by @gregorysprenger in #56
Concatenate kraken summaries and place in summary directory by @gregorysprenger in #52
Add header to BLAST output file by @gregorysprenger in #51
Update output documentation by @gregorysprenger in #45
Patch for host removal and kraken2 db by @gregorysprenger in #50
FastQ Phred cutoff value option by @gregorysprenger in #35
Use MegaLinter to lint and attempt autofixing issues by @gregorysprenger in #55
Removing RDP warnings by @taylorpaisie in #62
Summarize QA files, convert tsv to xlsx, and create xlsx summary report by @gregorysprenger in #61
Fix rdp issue with output file names by @taylorpaisie in #66
Ignore FastA files when using gitleaks linter by @gregorysprenger in #67
update release version to 2.2.0 by @chrisgulvik in #68

Full Changelog: v2.1.0...v2.2.0

Contributors

chrisgulvik, taylorpaisie, and gregorysprenger

Assets 2

26 Jan 15:41

chrisgulvik

v2.1.0

17aa18c

v2.1.0

What's Changed

Merge fix by @taylorpaisie in #18
untested, 2 new modules for host removal; related to issue #5 by @chrisgulvik in #19
Misc issue template by @taylorpaisie in #23
Update .nf-core.yml to ignore nf-core specific tests by @gregorysprenger in #24
Fix broken links by @gregorysprenger in #25
Use meta.id on database names by @gregorysprenger in #26
Update nf-core gtdbtk and busco module by @gregorysprenger in #29
Fix parsing of data from PhiX removal by @gregorysprenger in #30
Force raw integers and avoid scientific notation by @gregorysprenger in #31
Dev host removal by @chrisgulvik in #33
Dev host removal by @chrisgulvik in #34
revert pull request #34 by @chrisgulvik in #38
New host by @chrisgulvik in #41
add host removal from dev into main branch, version release bump by @chrisgulvik in #43