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Develop -> master #375

Merged
merged 16 commits into from
Jun 9, 2020
Merged

Develop -> master #375

merged 16 commits into from
Jun 9, 2020

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Maarten-vd-Sande
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Let's put it on master so I can get started with a bioconda package

siebrenf and others added 16 commits June 1, 2020 13:56
@siebrenf
Update merge_replicates.smk
df036dc
@Maarten-vd-Sande
Merge branch 'master' into develop
e33430c
@Maarten-vd-Sande
Merge branch 'master' into develop
d3b4df4
@siebrenf
drop descriptive names from treps (#368)
69b1c66
@siebrenf
Fix#355 (#369)
42c0f15 
* drop descriptive names from treps

* created config with salmon decoy aware indexing

* prevent @ from entering dir string
@siebrenf
new directories seem to have fixed this
730ea41
@Maarten-vd-Sande
continuous deployment (#360)
dd72624
@Maarten-vd-Sande
Multiqc thingies (#371)
ec0bb5b 
* samples & config in report

* working example

* why did I have to add bs4?

* Update requirements.yaml
@siebrenf @Maarten-vd-Sande
configuration_generic.smk (#372)
fc17b53 
* resolved #341 

* reorganized code in configuration_generic.smk by section: config.yaml, samples.tsv, samples and workflow. 

* updated gitignore. 

* seq2science now uses mamba by default

* fixed bug. profile cores no longer overwrite user cores

Co-authored-by: Maarten-vd-Sande <Maarten-vd-Sande@users.noreply.github.com>
@Maarten-vd-Sande
Sample filters, fixes #350 (#374)
c7e9255 
* fix #363

* fix #351

* fix #350
@siebrenf
Get annotation (#376)
5696bf3 
* removed get_annotation dependency

* fixed ChildIOException error
@Maarten-vd-Sande
Update requirements.yaml (#380)
3d4a8d3
@Maarten-vd-Sande
Update requirements.yaml (#383)
1f439fa
@Maarten-vd-Sande
fix #332, but still expects the blacklist present (#382)
f42647e
@Maarten-vd-Sande @siebrenf
use seq2science instead of snakemake (#373)
8dd5d56 
* fix #363, #351

* s2s can now accept lists are options input, e.g.: --snakemakeOptions until=[get_genome].

* allow @ symbol on Jenkins

* all tests now use the seq2science wrapper

Co-authored-by: siebrenf <48289046+siebrenf@users.noreply.github.com>
Co-authored-by: siebrenf <siebrenf@gmail.com>
@siebrenf
fix #356, fix #354 (#385)
cbaa457
@Maarten-vd-Sande Maarten-vd-Sande merged commit d4b79ab into master Jun 9, 2020
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2 participants
@Maarten-vd-Sande @siebrenf