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feat: adds GRCm39 to default_effective_genome_size
in deepTools bamCoverage
#3164
feat: adds GRCm39 to default_effective_genome_size
in deepTools bamCoverage
#3164
Conversation
the `default_effective_genome_size` dict in `wrapper.py` includes the key-value pair `"250": <effective_genome_size>` for all available genomes, but it was missing from the params
WalkthroughThe changes involve updates to the Changes
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Actionable comments posted: 0
Review details
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Review profile: CHILL
Files selected for processing (2)
- bio/deeptools/bamcoverage/meta.yaml (1 hunks)
- bio/deeptools/bamcoverage/wrapper.py (1 hunks)
Additional context used
Path-based instructions (1)
bio/deeptools/bamcoverage/wrapper.py (2)
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Additional comments not posted (3)
bio/deeptools/bamcoverage/meta.yaml (2)
15-15
: Addition of GRCm39 to genome options.The inclusion of
GRCm39
alongside other genome versions likeGRCm37
andGRCm38
is consistent and expands the tool's applicability to newer genome assemblies.The code changes are approved.
16-16
: Expansion of read length options to include 250.Adding
250
to theread_length
options aligns with the PR's objective to reflect the existing code capabilities in the documentation, enhancing user flexibility in specifying read lengths.The code changes are approved.
bio/deeptools/bamcoverage/wrapper.py (1)
45-51
: Addition of GRCm39 to effective genome size mapping.The inclusion of
GRCm39
with specific values for different read lengths (50
,75
,100
,150
,200
,250
) is consistent with the structure used for other genome assemblies. This addition enhances the tool's functionality by supporting a newer genome assembly.The code changes are approved.
🤖 I have created a release \*beep\* \*boop\* --- ## [4.4.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.3.0...v4.4.0) (2024-09-17) ### Features * adds GRCm39 to `default_effective_genome_size` in deepTools bamCoverage ([#3164](https://www.github.com/snakemake/snakemake-wrappers/issues/3164)) ([b5916c4](https://www.github.com/snakemake/snakemake-wrappers/commit/b5916c4bff9e3ab009bf57ff66873770b344cf0d)) * Bwameth index ([#3162](https://www.github.com/snakemake/snakemake-wrappers/issues/3162)) ([bb4acf9](https://www.github.com/snakemake/snakemake-wrappers/commit/bb4acf978165278a1dac14b86c98ffecd1534b29)) ### Performance Improvements * autobump bio/adapterremoval ([#3144](https://www.github.com/snakemake/snakemake-wrappers/issues/3144)) ([ddebbec](https://www.github.com/snakemake/snakemake-wrappers/commit/ddebbece33b3e7d95abed984ac7ceb6277209379)) * autobump bio/bcftools/call ([#3188](https://www.github.com/snakemake/snakemake-wrappers/issues/3188)) 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bio/samtools/sort ([#3230](https://www.github.com/snakemake/snakemake-wrappers/issues/3230)) ([65f98d3](https://www.github.com/snakemake/snakemake-wrappers/commit/65f98d377b954b828c2081c8019f04a335d27f13)) * autobump bio/samtools/stats ([#3238](https://www.github.com/snakemake/snakemake-wrappers/issues/3238)) ([da97159](https://www.github.com/snakemake/snakemake-wrappers/commit/da97159e3523590c3a1a57f1d7dcdc3e4d0597f5)) * autobump bio/samtools/view ([#3233](https://www.github.com/snakemake/snakemake-wrappers/issues/3233)) ([69514b5](https://www.github.com/snakemake/snakemake-wrappers/commit/69514b5966155d32b0a199efc3647449613b2136)) * autobump bio/snpeff/annotate ([#3226](https://www.github.com/snakemake/snakemake-wrappers/issues/3226)) ([01a432e](https://www.github.com/snakemake/snakemake-wrappers/commit/01a432ed553a2a1d1ae783f9170d331e28616a83)) * autobump bio/snpeff/download ([#3228](https://www.github.com/snakemake/snakemake-wrappers/issues/3228)) 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bio/ucsc/bedGraphToBigWig ([#3160](https://www.github.com/snakemake/snakemake-wrappers/issues/3160)) ([a8c4f3b](https://www.github.com/snakemake/snakemake-wrappers/commit/a8c4f3bc9183e161ed1721a520471fd72bc16d2b)) * autobump bio/ucsc/faToTwoBit ([#3156](https://www.github.com/snakemake/snakemake-wrappers/issues/3156)) ([5745452](https://www.github.com/snakemake/snakemake-wrappers/commit/5745452ca8ef5567b8df2f6187836d47a29925d9)) * autobump bio/ucsc/genePredToBed ([#3158](https://www.github.com/snakemake/snakemake-wrappers/issues/3158)) ([8f1db22](https://www.github.com/snakemake/snakemake-wrappers/commit/8f1db225877c81932da88893624a4dcc60e052ee)) * autobump bio/ucsc/gtfToGenePred ([#3159](https://www.github.com/snakemake/snakemake-wrappers/issues/3159)) ([6faa0c6](https://www.github.com/snakemake/snakemake-wrappers/commit/6faa0c6fb9d21a62d17fc773e213bc857c83c139)) * autobump bio/ucsc/twoBitInfo ([#3157](https://www.github.com/snakemake/snakemake-wrappers/issues/3157)) 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([#3242](https://www.github.com/snakemake/snakemake-wrappers/issues/3242)) ([105e474](https://www.github.com/snakemake/snakemake-wrappers/commit/105e474d60b98787ad49b5f3720a7256e8bac07a)) * autobump bio/vg/kmers ([#3245](https://www.github.com/snakemake/snakemake-wrappers/issues/3245)) ([ffab8f4](https://www.github.com/snakemake/snakemake-wrappers/commit/ffab8f466a9aef907ad51344326b2de0f5a8f40e)) * autobump bio/vg/merge ([#3247](https://www.github.com/snakemake/snakemake-wrappers/issues/3247)) ([20defe3](https://www.github.com/snakemake/snakemake-wrappers/commit/20defe34945248316d7fb0dae58f40d9531835c0)) * autobump bio/vg/prune ([#3243](https://www.github.com/snakemake/snakemake-wrappers/issues/3243)) ([60a29bf](https://www.github.com/snakemake/snakemake-wrappers/commit/60a29bf1f76b6dadaf3a9636eca9d9cc5a44dd68)) * autobump bio/vg/sim ([#3246](https://www.github.com/snakemake/snakemake-wrappers/issues/3246)) 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The deepTools documentation provides the effective genome size by read length for GRCm39, so I added it to the
default_effective_genome_size
dictionary in the deepTools bamCoverage wrapper. I've also made minor adjustments to theparams
in the "meta.yaml" file - i.e., added GRCm39 togenome
, and 250 toread_length
(which was already allowed in the code but missing from the docs).QC
snakemake-wrappers
.While the contributions guidelines are more extensive, please particularly ensure that:
test.py
was updated to call any added or updated example rules in aSnakefile
input:
andoutput:
file paths in the rules can be chosen arbitrarilyinput:
oroutput:
)tempfile.gettempdir()
points tometa.yaml
contains a link to the documentation of the respective tool or command underurl:
Summary by CodeRabbit
GRCm39
genome assembly in the configuration options.read_length
parameter to include a new option of250
.These updates enhance flexibility and functionality for users working with genomic data.