Comments (1)
That is most likely because you're running the pipeline as nextflow run distiller.nf -params-file ...
without -resume
option. In such case nextflow
relies only on the results that are in the intermediates
(which are stored there by the means of storeDir
directive), but fastqc
process does not have such a directive https://github.com/mirnylab/distiller-nf/blob/09a9b41567587384ccb39c76da49f7986f381789/distiller.nf#L133 , and stores the results only in work
folder and in the output
. Contents of the work
folder should be taken into account by the nextflow
processes that are not using storeDir
, when re-running pipeline with resume: nextflow run distiller.nf -resume -params-file ...
.
Overall this is related to #52 #31 #41 and the ongoing debate @golobor on how to best organize distiller
outputs, while minimizing disk usage and maximizing user-convenience.
from distiller-nf.
Related Issues (20)
- where can I get the specific instructions of the software
- Error when trying to run on test dataset HOT 13
- process from 4DN?
- Running without duplicates filtering HOT 11
- Remove duplicate reads in sam/bam files
- Error: Process `map_parse_sort_chunks (library:HSPR2 run:lane1 chunk:0)` terminated with an error exit status (140) HOT 4
- distiller-nf run failed at executing process > 'bin_zoom_library_pairs‘ HOT 1
- Bug: split: output file suffixes exhausted
- Iterative mapping HOT 2
- Optional direct fastq downloads from ENA instead of sra-tools
- how memory limit gets specified in cluster using
- library (group) names can't be numerical
- bam files recycling
- update example cluster config - to match current distiller HOT 1
- Support of minimap2, bam mem2 and bwa aln HOT 1
- distiller 0.3.5 roadmap HOT 1
- filter with non-int columns
- which reference should I cite? HOT 1
- Help with "Error executing process > 'map_parse_sort_chunks...' HOT 4
- Skip deduplication for libraries with UMI
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from distiller-nf.