Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub / xiaoli-dong / pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xiaoli-dong%2Fpathogenseq

Stars: 2
Forks: 1
Open Issues: 1

License: mit
Language: Nextflow
Repo Size: 2.47 MB
Dependencies: 20

Created: 11 months ago
Updated: 20 days ago
Last pushed: 20 days ago
Last synced: 20 days ago

Commit Stats

Commits: 151
Authors: 5
Mean commits per author: 30.2
Development Distribution Score: 0.331
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/xiaoli-dong/pathogenseq

Topics: amr, assembly, capsular-typing, emm-typing, illumina, mlst, nanopore, ngs, pathogen, plasmid, serotyping, taxonomy, virulome

Files

Readme

Dependencies

.github/workflows/awsfulltest.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v3 composite
nf-core/setup-nextflow v1 composite

.github/workflows/clean-up.yml actions

actions/stale v7 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite

.github/workflows/linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
mshick/add-pr-comment v1 composite
nf-core/setup-nextflow v1 composite
psf/black stable composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

modules/nf-core/abricate/run/meta.yml cpan

modules/nf-core/abricate/summary/meta.yml cpan

modules/nf-core/amrfinderplus/update/meta.yml cpan

modules/nf-core/bakta/bakta/meta.yml cpan

modules/nf-core/bbmap/bbduk/meta.yml cpan

modules/nf-core/csvtk/concat/meta.yml cpan

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/fastp/meta.yml cpan

modules/nf-core/fastqc/meta.yml cpan

modules/nf-core/flye/meta.yml cpan

modules/nf-core/kraken2/kraken2/meta.yml cpan

modules/nf-core/krakentools/combinekreports/meta.yml cpan

modules/nf-core/medaka/meta.yml cpan

modules/nf-core/megahit/meta.yml cpan

modules/nf-core/mlst/meta.yml cpan

modules/nf-core/nanoplot/meta.yml cpan

modules/nf-core/porechop/porechop/meta.yml cpan

modules/nf-core/samtools/index/meta.yml cpan

modules/nf-core/samtools/sort/meta.yml cpan

modules/nf-core/samtools/view/meta.yml cpan

modules/nf-core/spades/meta.yml cpan

modules/nf-core/unicycler/meta.yml cpan

pyproject.toml pypi

modules/local/medaka/meta.yml cpan

modules/nf-core/samtools/coverage/meta.yml cpan

modules/local/shovill/meta.yml cpan

modules/local/shovill/environment.yml conda

shovill 1.1.0.*

modules/local/bwamem2/index/meta.yml cpan

modules/local/bwamem2/mem/meta.yml cpan

modules/local/csvtk/add-header/meta.yml cpan

modules/local/csvtk/concat/meta.yml cpan

modules/local/emmtyper/meta.yml cpan

modules/local/fastp/meta.yml cpan

modules/local/pneumocat/meta.yml cpan

modules/local/tbprofiler/profile/meta.yml cpan

modules/nf-core/abritamr/run/meta.yml cpan

modules/nf-core/bwamem2/index/meta.yml cpan

modules/nf-core/bwamem2/mem/meta.yml cpan

modules/nf-core/emmtyper/meta.yml cpan

modules/local/bwamem2/index/environment.yml pypi

modules/local/bwamem2/mem/environment.yml pypi

modules/local/csvtk/add-header/environment.yml pypi

modules/local/emmtyper/environment.yml pypi

modules/local/pneumocat/environment.yml pypi

modules/local/tbprofiler/profile/environment.yml pypi

modules/nf-core/abritamr/run/environment.yml pypi

modules/nf-core/bwamem2/index/environment.yml pypi

modules/nf-core/bwamem2/mem/environment.yml pypi

modules/nf-core/emmtyper/environment.yml pypi

modules/nf-core/fastp/environment.yml pypi