Running the Pipeline
Quick Start
Check prerequisites
$ nextflow -v
nextflow version 23.04.1.5866
$ docker -v
Docker version 24.0.4, build 3713ee1
Notice that your installed version might differ with the example here.
Run the minimal test dataset
nextflow run nf-core/pixelator -profile test,docker --outdir "./results"
N E X T F L O W ~ version 23.04.3
Launching `https://github.com/nf-core/pixelator` [hopeful_mendel] DSL2 - revision: 979b3e59cb [dev]
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nf-core/pixelator v1.0.0dev-g979b3e5
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Core Nextflow options
revision : dev
runName : hopeful_mendel
containerEngine : docker
launchDir : /home/fbdtemme
workDir : /home/fbdtemme/work
projectDir : /home/fbdtemme/.nextflow/assets/nf-core/pixelator
userName : fbdtemme
profile : docker,test
configFiles :
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/samplesheet/samplesheet.csv
input_basedir : https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata
outdir : example
Options for pixelator annotate command.
min_size : 2
max_size : 100000
Options for pixelator analysis command.
use_full_bipartite : true
colocalization_n_permutations : 10
colocalization_min_region_count: 0
Institutional config options
config_profile_name : Test profile
config_profile_description : Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/pixelator for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
Resolving relative paths in samplesheet relative to: https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata/
executor > local (16)
[a2/4f1f37] process > NFCORE_PIXELATOR:PIXELATOR:INPUT_CHECK:PIXELATOR_LIST_OPTIONS [100%] 1 of 1 ✔
[f8/16fcf7] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLECT_METADATA [100%] 1 of 1 ✔
[- ] process > NFCORE_PIXELATOR:PIXELATOR:CAT_FASTQ -
[cb/fddf68] process > NFCORE_PIXELATOR:PIXELATOR:RENAME_READS (uropod_control) [100%] 2 of 2 ✔
[64/d09f9f] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_AMPLICON (uropod_control) [100%] 2 of 2 ✔
[6f/f4d468] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_QC (uropod_control) [100%] 2 of 2 ✔
[03/c0978a] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_DEMUX (uropod_control) [100%] 2 of 2 ✔
[8c/0b42a5] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_COLLAPSE (uropod_control) [100%] 2 of 2 ✔
[4b/56e05c] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_GRAPH (uropod_control) [100%] 2 of 2 ✔
[10/ff8b6c] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ANNOTATE (uropod_control) [ 0%] 0 of 2
[- ] process > NFCORE_PIXELATOR:PIXELATOR:PIXELATOR_ANALYSIS -
[- ] process > NFCORE_PIXELATOR:PIXELATOR:GENERATE_REPORTS:PIXELATOR_REPORT -
[- ] process > NFCORE_PIXELATOR:PIXELATOR:CUSTOM_DUMPSOFTWAREVERSIONS -
At this point you should see that nextflow has downloaded the project code locally to ~/.nextflow/assets so it can be reused in every run:
$ nextflow list
nf-core/pixelator
The information associated to this project and the folder where the project resides can be easily found:
$ nextflow info nf-core/pixelator
project name: nf-core/pixelator
repository : https://github.com/nf-core/pixelator
local path : /home/fbdtemme/.nextflow/assets/nf-core/pixelator
main script : main.nf
description : Pipeline for analysis of Molecular Pixelation assays
author : Pixelgen Technologies AB
revisions :
* master
dev
TEMPLATE
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Start running your own analysis with your MPX data
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Make sure you keep your pipeline updated with the latest features
Run a full dataset
If you want to test your configuration on a real-world example, feel free to use one of our public datasets. Below we will demonstrate how to execute the pipeline with data from the 1k Human PBMCs dataset. Begin by obtaining a copy of the samplesheet, then make sure the latest version of the pipeline has been downloaded:
nextflow pull nf-core/pixelator
Finally, pass the following command to start the pipeline using the default parameters:
nextflow run nf-core/pixelator \
-profile docker \
--input samplesheet.1k-human-pbmcs.csv \
--outdir "./results"