DSL2 implementation - Githubissues

nf-core / hic

Analysis of Chromosome Conformation Capture data (Hi-C)

https://nf-co.re/hic

MIT License

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DSL2 implementation #119

Closed nservant closed 1 year ago

nservant commented 2 years ago

TODO list/checks for DSL2 implementation

input

[x] merge multiple runs
[x] split_fastq files

hicpro

[x] dnase mode
[x] ch_versions
[x] stats folder
[x] MultiQC
[ ] clean some steps
[x] move to python 3.9
[x] > 0

cooler

[x] PR for cooler modules updates ?

modules

[x] add new cooler in the DSL2 modules
[ ] add new cooltools in the DSL2 modules
[ ] add new hicexplorer in the DSL2 modules
[ ] Check multiQC module

env

[x] conda
[x] singularity
[x] docker

test

[x] small test
[ ] larger test

lint

[x] nf-core linting

nservant commented 2 years ago

would be great to update the MultiQC module then ... especially because so far it requires the log files to be in a folder with the sample name ... a bit painfull to work with