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feat: Goleft indexcov #2734

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May 7, 2024
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ab82604
[fix] (template): Missing code in wrappers' doc. Error #187
Sep 21, 2020
de77ade
Merge remote-tracking branch 'upstream/master'
Nov 9, 2020
9b1447e
Merge branch 'snakemake:master' into master
tdayris Jul 2, 2021
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tdayris Apr 29, 2022
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Jun 27, 2022
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Oct 11, 2022
ac4ac81
perf: update utils/datavzrd/environment.yaml. (#566)
johanneskoester Oct 11, 2022
88c479c
perf: update bio/bcftools/call/environment.yaml. (#567)
johanneskoester Oct 11, 2022
8d92bb5
perf: update bio/bcftools/concat/environment.yaml. (#568)
johanneskoester Oct 11, 2022
1c444dc
perf: autobump bio/bcftools/index/environment.yaml (#570)
johanneskoester Oct 11, 2022
534f834
chore: release 1.15.1 (#569)
github-actions[bot] Oct 12, 2022
7eb277c
perf: update bio/bgzip/environment.yaml. (#577)
snakedeploy-bot[bot] Oct 12, 2022
63f8acb
perf: update bio/bellerophon/environment.yaml. (#576)
snakedeploy-bot[bot] Oct 12, 2022
963bedf
perf: update bio/assembly-stats/environment.yaml. (#575)
snakedeploy-bot[bot] Oct 12, 2022
ff74710
perf: update bio/adapterremoval/environment.yaml. (#573)
snakedeploy-bot[bot] Oct 12, 2022
bb60c16
chore: autobump conda envs (#571)
johanneskoester Oct 12, 2022
d9a7a6a
perf: update bio/delly/environment.yaml. (#584)
snakedeploy-bot[bot] Oct 12, 2022
e0220d2
perf: update bio/busco/environment.yaml. (#581)
snakedeploy-bot[bot] Oct 12, 2022
ae10993
perf: update bio/clustalo/environment.yaml. (#582)
snakedeploy-bot[bot] Oct 12, 2022
76c9845
perf: update bio/fastp/environment.yaml. (#585)
snakedeploy-bot[bot] Oct 12, 2022
853a36d
perf: update bio/fastq_screen/environment.yaml. (#586)
snakedeploy-bot[bot] Oct 12, 2022
576c54a
perf: update bio/fasttree/environment.yaml. (#588)
snakedeploy-bot[bot] Oct 12, 2022
e473ff7
perf: update bio/fastqc/environment.yaml. (#587)
snakedeploy-bot[bot] Oct 12, 2022
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perf: update bio/filtlong/environment.yaml. (#589)
snakedeploy-bot[bot] Oct 12, 2022
5a1f598
perf: update bio/freebayes/environment.yaml. (#590)
snakedeploy-bot[bot] Oct 12, 2022
f60db66
perf: update bio/genefuse/environment.yaml. (#591)
snakedeploy-bot[bot] Oct 12, 2022
cb6b616
perf: update bio/genomepy/environment.yaml. (#592)
snakedeploy-bot[bot] Oct 12, 2022
f618f0d
chore: release 1.15.2 (#578)
github-actions[bot] Oct 12, 2022
141e09e
fix: set RG tag (#593)
FelixMoelder Oct 13, 2022
278f508
Update conventional-prs.yml
johanneskoester Oct 13, 2022
de6ce85
perf: autobump bio/deepvariant (#583)
snakedeploy-bot[bot] Oct 13, 2022
f9332c2
feat: bazam wrapper (#580)
christopher-schroeder Oct 13, 2022
39c488d
chore: release 1.16.0 (#596)
github-actions[bot] Oct 13, 2022
d1a68e5
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tdayris Nov 24, 2023
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tdayris Feb 28, 2024
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Merge branch 'snakemake:master' into master
tdayris Mar 6, 2024
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initial commit
Mar 11, 2024
ea3d214
pin & clean
Mar 11, 2024
06ecbba
Update bio/goleft/indexcov/wrapper.py
tdayris Mar 11, 2024
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Conding scheme
Mar 12, 2024
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Mar 12, 2024
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Merge branch 'master' into goleft
tdayris Mar 14, 2024
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Update bio/goleft/indexcov/wrapper.py
tdayris May 7, 2024
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May 7, 2024
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tdayris May 7, 2024
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28 changes: 28 additions & 0 deletions bio/goleft/indexcov/environment.linux-64.pin.txt
Original file line number Diff line number Diff line change
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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb
https://conda.anaconda.org/bioconda/linux-64/htslib-1.19.1-h81da01d_2.tar.bz2#ad57eedd99d6722b2f00a8f7d0d71e2a
https://conda.anaconda.org/bioconda/linux-64/samtools-1.19.2-h50ea8bc_1.tar.bz2#446e85653117e24527bc4ba6d3841d8b
https://conda.anaconda.org/bioconda/linux-64/goleft-0.2.4-h9ee0642_1.tar.bz2#a8658992b88c9323cff55ea1237a7103
6 changes: 6 additions & 0 deletions bio/goleft/indexcov/environment.yaml
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@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- goleft=0.2.4
19 changes: 19 additions & 0 deletions bio/goleft/indexcov/meta.yaml
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name: "goleft indexcov"
description: "Quickly estimate coverage from a whole-genome bam or cram index"
url: "https://github.com/brentp/goleft/tree/master/indexcov#indexcov"
authors:
- "Thibault Dayris"
input:
- aln: Path to indexed BAM/CRAM file
- fai: Path to fasta sequence index
output:
- html: Optional path to HTML report
- bed: Optional path to coverage bed
- ped: Optional path to pedigree file
- roc: Optional path to coverage curves
params:
- extra: Optional parameters besides `-d` or `-r`
notes: |
Coverage bed, pedigree file, and roc curves are available in the HTML report.
Using `bed`, `ped`, or `roc` output keys alongside with `html` will make these
results unavailable in the HTML report, but won't break HTML content display.
15 changes: 15 additions & 0 deletions bio/goleft/indexcov/test/Snakefile
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rule test_goleft_indexcov:
input:
aln="sample.bam",
fai="genome.fai",
output:
bed="regions.bed.gz",
ped="indexcov.ped",
roc="indexcov.roc",
html=directory("report"),
log:
"indexcov.log",
params:
extra="-e",
wrapper:
"master/bio/goleft/indexcov"
20 changes: 20 additions & 0 deletions bio/goleft/indexcov/test/genome.fai
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10 135534747 1708379889 60 61
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12 133851895 1983430282 60 61
13 115169878 2119513096 60 61
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16 90354753 2449981581 60 61
17 81195210 2541842300 60 61
18 78077248 2624390817 60 61
19 59128983 2703769406 60 61
20 63025520 2763883926 60 61
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