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Update Kraken2, fastp, kajiu, bbmap
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boulund committed Nov 16, 2021
1 parent deb3ea5 commit 1c43e12
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10 changes: 8 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -18,15 +18,17 @@ situations.
### Added
- Biobakery update: updated MetaPhlAn and HUMAnN to version 3 as well as introducing
StrainPhlAn3 for strain-level genomics.
- Added $TMPDIR variable which can be specified in config.yaml. It is normally not required
to specify $TMPDIR but might be necessary to run HUMAnN due to large intermediary files.
- Added `$TMPDIR` variable which can be specified in config.yaml. It is normally not required
to specify `$TMPDIR` but might be necessary to run HUMAnN due to large intermediary files.
- New internal StaG feature to better handle user messages and defer them for printing after
the workflow finished execution so they don't get lost in the verbose log printout from
Snakemake.
- Added new feature to automatically remove intermediaries with the use of
`keep_` flags in the config file. Currently available for Quality control
(fastp), host removal (kraken2), taxonomic profiling with Kraken2 and
MetaPhlAn3.
- Automatic builds of Singularity images using Github actions. Images get uploaded to
the Github Package repository at `ghcr.io/ctmrbio/stag-mwc:<tag>-<branch>`.

### Fixed
- Updated pandas to 1.2.1 to fix issue with `preprocessing_summary.py` failing.
Expand All @@ -38,6 +40,10 @@ situations.
- Limited job allocations to one node in `ctmr_gandalf` cluster config.

### Changed
- Updated Kraken2 to 2.1.2 and added `--minimum-hit-groups` argument in config file.
- Updated fastp to 0.23.0.
- Updated Kaiju to 1.8.2.
- Updated BBMap to 38.93.

### Removed

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1 change: 1 addition & 0 deletions config.yaml
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Expand Up @@ -88,6 +88,7 @@ kaiju:
kraken2:
db: "" # [Required] Path to Kraken2 DB folder
confidence: 0.1 # Kraken2 confidence score, float in [0,1]
minimum_hit_groups: 2 # Integer, default 2
extra: "" # Extra command line arguments for kraken2 (do not add/change output files)
keep_kraken: False # Keep the kraken output files
keep_kreport: True # Keep the kreport output files
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6 changes: 3 additions & 3 deletions envs/stag-mwc.yaml
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Expand Up @@ -5,9 +5,9 @@ channels:
- defaults
dependencies:
- python =3.7
- fastp =0.20.0
- bbmap =38.68
- kaiju =1.7.2
- fastp =0.23.0
- bbmap =38.93
- kaiju =1.8.2
- kraken2 =2.1.2
- bracken =2.5
- krona =2.7
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2 changes: 2 additions & 0 deletions rules/taxonomic_profiling/kraken2.smk
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Expand Up @@ -93,12 +93,14 @@ rule kraken2:
params:
db=kraken2_config["db"],
confidence=kraken2_config["confidence"],
minimum_hit_groups=kraken2_config["minimum_hit_groups"],
extra=kraken2_config["extra"],
shell:
"""
kraken2 \
--db {params.db} \
--confidence {params.confidence} \
--minimum-hit-groups {params.minimum_hit_groups} \
--threads {threads} \
--output {output.kraken} \
--report {output.kreport} \
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