snakepipes

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Some arguments should be removed or verified since 3.0, i.e.: - clusterConfig -> remove - maxJobs -> verify - .. ?

WardDeb

version 3.0.0 fails to create environments (stops at the RNAseq)

5

the envs/shared.yaml and envs/createIndices.yaml are created without issues. but the whole process just fails in the next level ```bash Creating environment (3/24) from envs/rna_seq.yaml with hash 7b098b94bad80d0be19669458b1d7ef9 Channels: - conda-forge...

sunta3iouxos

resources/--j

1

Hi, Thanks for the active development of snakePipes :) I noticed that in the version 3.0.0, there is no longer the option --local and --j. Could you explain how can...

hanrong498

Sambamba markdup log is needed for MultiQC report, this changes captures that and renamed the flagstat outptus

caballero

default conda env in 3.0.0

4

Hi all, Even in I set the `snakePipes config --condaEnvDir /scratch/tgeorgom/mamba/snakePipes/env --tempDir /scratch/tgeorgom/temp` while riunning the snakePipes createEnvs``, snakePipes creates a folder into /tmp, that I have no access to....

sunta3iouxos

Internally reported: combine_loom rule doesn't properly create it's output dir, resulting in 'file not exists' error.

WardDeb

katsikora

conda-env create is using /tmp

7

snakePipes 3.0.0 - snakemake is calling conda create env and pointing it to /tmp rather than to condaEnvDir defined in the defaults.yaml

katsikora

snakePipes 3.0.0 logging

4

I get no logs, and the numbered run logs are empty.

katsikora

In you ATAC-seq pipeline the default seting for the --maxFragmentSize is 150. This setting will exclude the mono-di-tri-nucleosomes that provide also a very good overview of the state of chromatin....

sunta3iouxos