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GitHub / maxulysse / nf-core_sarek

Main repo:

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxulysse%2Fnf-core_sarek

Fork of nf-core/sarek
Stars: 5
Forks: 2
Open Issues: 0

License: mit
Language: Nextflow
Repo Size: 39.6 MB
Dependencies: 29

Created: over 7 years ago
Updated: about 1 month ago
Last pushed: about 1 month ago
Last synced: about 1 month ago

Files

Readme

Dependencies

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
nf-core/tower-action v3 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

Wandalen/wretry.action v1.0.11 composite
actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v2 composite
actions/upload-artifact v2 composite
conda-incubator/setup-miniconda v2 composite
eWaterCycle/setup-singularity v5 composite
nf-core/setup-nextflow v1.2.0 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

.github/workflows/clean-up.yml actions

actions/stale v7 composite

.github/workflows/release-announcments.yml actions

actions/setup-python v4 composite
rzr/fediverse-action master composite
zentered/bluesky-post-action v0.0.2 composite

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

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

modules/nf-core/bcftools/mpileup/meta.yml cpan

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

modules/nf-core/bcftools/stats/meta.yml cpan

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

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

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

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

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

modules/nf-core/cat/fastq/meta.yml cpan

modules/nf-core/cnvkit/antitarget/meta.yml cpan

modules/nf-core/cnvkit/batch/meta.yml cpan

modules/nf-core/cnvkit/reference/meta.yml cpan

modules/nf-core/controlfreec/assesssignificance/meta.yml cpan

modules/nf-core/controlfreec/freec/meta.yml cpan

modules/nf-core/controlfreec/freec2bed/meta.yml cpan

modules/nf-core/controlfreec/freec2circos/meta.yml cpan

modules/nf-core/controlfreec/makegraph/meta.yml cpan

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

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

modules/nf-core/dragmap/align/meta.yml cpan

modules/nf-core/dragmap/hashtable/meta.yml cpan

modules/nf-core/ensemblvep/download/meta.yml cpan

modules/nf-core/ensemblvep/vep/meta.yml cpan

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

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

modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml cpan

modules/nf-core/fgbio/fastqtobam/meta.yml cpan

modules/nf-core/fgbio/groupreadsbyumi/meta.yml cpan

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

modules/nf-core/gatk4/applybqsr/meta.yml cpan

modules/nf-core/gatk4/applybqsrspark/meta.yml cpan

modules/nf-core/gatk4/applyvqsr/meta.yml cpan

modules/nf-core/gatk4/baserecalibrator/meta.yml cpan

modules/nf-core/gatk4/baserecalibratorspark/meta.yml cpan

modules/nf-core/gatk4/calculatecontamination/meta.yml cpan

modules/nf-core/gatk4/cnnscorevariants/meta.yml cpan

modules/nf-core/gatk4/createsequencedictionary/meta.yml cpan

modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml cpan

modules/nf-core/gatk4/filtermutectcalls/meta.yml cpan

modules/nf-core/gatk4/filtervarianttranches/meta.yml cpan

modules/nf-core/gatk4/gatherbqsrreports/meta.yml cpan

modules/nf-core/gatk4/gatherpileupsummaries/meta.yml cpan

modules/nf-core/gatk4/genomicsdbimport/meta.yml cpan

modules/nf-core/gatk4/genotypegvcfs/meta.yml cpan

modules/nf-core/gatk4/getpileupsummaries/meta.yml cpan

modules/nf-core/gatk4/haplotypecaller/meta.yml cpan

modules/nf-core/gatk4/intervallisttobed/meta.yml cpan

modules/nf-core/gatk4/learnreadorientationmodel/meta.yml cpan

modules/nf-core/gatk4/markduplicates/meta.yml cpan

modules/nf-core/gatk4/markduplicatesspark/meta.yml cpan

modules/nf-core/gatk4/mergemutectstats/meta.yml cpan

modules/nf-core/gatk4/mergevcfs/meta.yml cpan

modules/nf-core/gatk4/mutect2/meta.yml cpan

modules/nf-core/gatk4/variantrecalibrator/meta.yml cpan

modules/nf-core/manta/germline/meta.yml cpan

modules/nf-core/manta/somatic/meta.yml cpan

modules/nf-core/manta/tumoronly/meta.yml cpan

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

modules/nf-core/msisensorpro/msisomatic/meta.yml cpan

modules/nf-core/msisensorpro/scan/meta.yml cpan

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

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

modules/nf-core/samtools/bam2fq/meta.yml cpan

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

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

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

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

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

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

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

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

modules/nf-core/sentieon/applyvarcal/meta.yml cpan

modules/nf-core/sentieon/bwamem/meta.yml cpan

modules/nf-core/sentieon/dedup/meta.yml cpan

modules/nf-core/sentieon/gvcftyper/meta.yml cpan

modules/nf-core/sentieon/haplotyper/meta.yml cpan

modules/nf-core/sentieon/varcal/meta.yml cpan

modules/nf-core/snpeff/download/meta.yml cpan

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

modules/nf-core/strelka/germline/meta.yml cpan

modules/nf-core/strelka/somatic/meta.yml cpan

modules/nf-core/svdb/merge/meta.yml cpan

modules/nf-core/tabix/bgziptabix/meta.yml cpan

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

modules/nf-core/tiddit/sv/meta.yml cpan

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

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

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

subworkflows/local/bam_joint_calling_germline_gatk/meta.yml cpan

subworkflows/local/bam_variant_calling_somatic_mutect2/meta.yml cpan

subworkflows/local/bam_variant_calling_tumor_only_mutect2/meta.yml cpan

subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml cpan

subworkflows/nf-core/vcf_annotate_snpeff/meta.yml cpan

pyproject.toml pypi

tests/requirements.txt pypi

cryptography * test
pip * test
pytest-workflow * test