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feat: add fgbio sorting to bwa mem #2805
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Can you add the test to |
fgvieira
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Apr 12, 2024
johanneskoester
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Apr 12, 2024
🤖 I have created a release \*beep\* \*boop\* --- ## [3.8.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.7.0...v3.8.0) (2024-04-12) ### Features * add fgbio sorting to bwa mem ([#2805](https://www.github.com/snakemake/snakemake-wrappers/issues/2805)) ([af98a55](https://www.github.com/snakemake/snakemake-wrappers/commit/af98a5591bc841b7fc829bcf71b9e4b2ebfe29d0)) * Add wrapper for ROOT hadd ([#2785](https://www.github.com/snakemake/snakemake-wrappers/issues/2785)) ([3e82e9c](https://www.github.com/snakemake/snakemake-wrappers/commit/3e82e9cd8a601d41381a870aee16cbdfb5072459)) ### Bug Fixes * bcftool stats bug ([#2806](https://www.github.com/snakemake/snakemake-wrappers/issues/2806)) ([e7ff82c](https://www.github.com/snakemake/snakemake-wrappers/commit/e7ff82cbe32d7ec8e296be3e21cb0653c3f1095d)) ### Performance Improvements * autobump bio/busco ([#2787](https://www.github.com/snakemake/snakemake-wrappers/issues/2787)) ([ebe243e](https://www.github.com/snakemake/snakemake-wrappers/commit/ebe243e751f40712bf3953a49c95d510b3680f14)) * autobump bio/deeptools/plotfingerprint ([#2776](https://www.github.com/snakemake/snakemake-wrappers/issues/2776)) ([214ea28](https://www.github.com/snakemake/snakemake-wrappers/commit/214ea28825991192f4f5f25b25f554eadfb15ec9)) * autobump bio/deeptools/plotheatmap ([#2788](https://www.github.com/snakemake/snakemake-wrappers/issues/2788)) ([81ee08b](https://www.github.com/snakemake/snakemake-wrappers/commit/81ee08b767737e66f4ef843fa7606d68d082e737)) * autobump bio/ega/fetch ([#2789](https://www.github.com/snakemake/snakemake-wrappers/issues/2789)) ([fd83ecb](https://www.github.com/snakemake/snakemake-wrappers/commit/fd83ecbeed2a36adc1170a41de59ed50202ee2e9)) * autobump bio/freebayes ([#1850](https://www.github.com/snakemake/snakemake-wrappers/issues/1850)) ([795e778](https://www.github.com/snakemake/snakemake-wrappers/commit/795e7781331c4e4bba56f055bc9c27d2b2167955)) * autobump bio/freebayes ([#2790](https://www.github.com/snakemake/snakemake-wrappers/issues/2790)) ([fe5de66](https://www.github.com/snakemake/snakemake-wrappers/commit/fe5de660110c8131d17ee27873a9c7f553133b36)) * autobump bio/gdc-api/bam-slicing ([#2778](https://www.github.com/snakemake/snakemake-wrappers/issues/2778)) ([9375ca8](https://www.github.com/snakemake/snakemake-wrappers/commit/9375ca8c718faf4b789633c5db768d247b59e93a)) * autobump bio/minimap2/aligner ([#2780](https://www.github.com/snakemake/snakemake-wrappers/issues/2780)) ([23fd5a3](https://www.github.com/snakemake/snakemake-wrappers/commit/23fd5a325964c7121ddeb218bad64630675e04db)) * autobump bio/minimap2/index ([#2779](https://www.github.com/snakemake/snakemake-wrappers/issues/2779)) ([8f5d611](https://www.github.com/snakemake/snakemake-wrappers/commit/8f5d61190bb7a711bba55e0c4591a8829e659964)) * autobump bio/plass ([#2791](https://www.github.com/snakemake/snakemake-wrappers/issues/2791)) ([11f34ca](https://www.github.com/snakemake/snakemake-wrappers/commit/11f34cad50399510051025aa157a4541ccb0b0f0)) * autobump bio/rseqc/read_gc ([#2781](https://www.github.com/snakemake/snakemake-wrappers/issues/2781)) ([842998d](https://www.github.com/snakemake/snakemake-wrappers/commit/842998dee3c213a4db315c472a98f5781734b394)) * autobump bio/seqkit ([#2795](https://www.github.com/snakemake/snakemake-wrappers/issues/2795)) ([1b2e7ba](https://www.github.com/snakemake/snakemake-wrappers/commit/1b2e7ba1b1163189cb617257a49f3e7492738f43)) * autobump bio/sourmash/compute ([#2794](https://www.github.com/snakemake/snakemake-wrappers/issues/2794)) ([8a37a3e](https://www.github.com/snakemake/snakemake-wrappers/commit/8a37a3e4fc29e3d63d8aa7d83cd9467382c4906d)) * autobump bio/tabix/query ([#2796](https://www.github.com/snakemake/snakemake-wrappers/issues/2796)) ([e21217e](https://www.github.com/snakemake/snakemake-wrappers/commit/e21217ebc139147e72424cd0a607907a3bf7f613)) * autobump bio/tmb/pytmb ([#2797](https://www.github.com/snakemake/snakemake-wrappers/issues/2797)) ([28ae8a8](https://www.github.com/snakemake/snakemake-wrappers/commit/28ae8a8d199235951617d164394e762b0453ebf9)) * autobump bio/ucsc/gtfToGenePred ([#2782](https://www.github.com/snakemake/snakemake-wrappers/issues/2782)) ([4e8c925](https://www.github.com/snakemake/snakemake-wrappers/commit/4e8c9252995e7ab3773c6dff6aee5e881bb2192f)) * autobump bio/unicycler ([#2316](https://www.github.com/snakemake/snakemake-wrappers/issues/2316)) ([0d1486b](https://www.github.com/snakemake/snakemake-wrappers/commit/0d1486b0b88b0f0077faf7533dc5d8b422e3af4d)) * autobump bio/vembrane/filter ([#2783](https://www.github.com/snakemake/snakemake-wrappers/issues/2783)) ([bb271ab](https://www.github.com/snakemake/snakemake-wrappers/commit/bb271abf6dbce49a9e86b5d299b2be8b0fca6df6)) * autobump bio/vembrane/table ([#2784](https://www.github.com/snakemake/snakemake-wrappers/issues/2784)) ([491d5b6](https://www.github.com/snakemake/snakemake-wrappers/commit/491d5b6273d8b341c1c9a898253ab196598a8b0a)) * autobump bio/vg/construct ([#2798](https://www.github.com/snakemake/snakemake-wrappers/issues/2798)) ([25300e4](https://www.github.com/snakemake/snakemake-wrappers/commit/25300e40f0b37ddc2e2c46534ef678b0a84d41c6)) * autobump bio/vg/ids ([#2804](https://www.github.com/snakemake/snakemake-wrappers/issues/2804)) ([4162ce1](https://www.github.com/snakemake/snakemake-wrappers/commit/4162ce1926b7bb2d5bdfa31315597f18125db791)) * autobump bio/vg/kmers ([#2802](https://www.github.com/snakemake/snakemake-wrappers/issues/2802)) ([9ddb88d](https://www.github.com/snakemake/snakemake-wrappers/commit/9ddb88d768a061b3dd9b3815c838fd5495b721b4)) * autobump bio/vg/merge ([#2800](https://www.github.com/snakemake/snakemake-wrappers/issues/2800)) ([5ba8325](https://www.github.com/snakemake/snakemake-wrappers/commit/5ba8325e54730a42096f29dc286de8fc615ed5ff)) * autobump bio/vg/prune ([#2801](https://www.github.com/snakemake/snakemake-wrappers/issues/2801)) ([2061beb](https://www.github.com/snakemake/snakemake-wrappers/commit/2061beb06a5bbf29ff5e095e1ac5803801a0fa22)) * autobump bio/vg/sim ([#2799](https://www.github.com/snakemake/snakemake-wrappers/issues/2799)) ([dfb0d6b](https://www.github.com/snakemake/snakemake-wrappers/commit/dfb0d6bf4f01bca68e221a08f08ed47fbaa739d4)) * autobump bio/vsearch ([#2803](https://www.github.com/snakemake/snakemake-wrappers/issues/2803)) ([7070607](https://www.github.com/snakemake/snakemake-wrappers/commit/7070607cb4e8bc233a55e20b62a2f019e63c9b00)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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In some cases sorting reads by
fgbio SortBam
is required as queryname sorting performed bysamtools
results in a different sorting order (see snakemake-workflows/dna-seq-varlociraptor#296). I therefore propose to addfgbio-minimal
as an addition to the wrapper.QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,environment.yaml
pinning has been updated by runningsnakedeploy pin-conda-envs environment.yaml
on a linux machine,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,