nallo good first issues (Nextflow)

Add custom GLNexus config to circumvent DP bug 3 months ago

enhancement good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace hiphase with nf-core module 4 months ago

good first issue Gain L Effort S Urgency L

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace echtvar/anno with nf-core module 4 months ago

good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Add input for fai index to allow for pre-built index 6 months ago

enhancement good first issue Gain S Effort S Urgency S

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

DeepVariant process tag should include region name, not only sample ID 7 months ago

enhancement good first issue Gain M Effort S Urgency S

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Split hifiasm process in two 7 months ago

enhancement good first issue Gain M Effort S Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Set default --min_indel_size to 50 in sawfish discover 8 months ago

enhancement good first issue

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Replace hardcoded Sniffles values in config with parameters 8 months ago

enhancement good first issue

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Update modkit to 0.6.1 8 months ago

good first issue Gain M Effort S Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace whatshap/haplotag with nf-core module 9 months ago

good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace whatshap/phase with nf-core module 10 months ago

good first issue Gain L Effort L Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace whatshap/stats with nf-core module 10 months ago

good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace pacbio/hificnv with nf-core module 11 months ago

good first issue Gain M Effort S Urgency S

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove spliceAI in pipeline tests 11 months ago

enhancement good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Replace build_intervals with gawk nf-core module 11 months ago

good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Typo in conf for DeepVariant 11 months ago

bug good first issue

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Change filter variants to a common (nf-core) `GENERATE_CLINICAL_SET` about 1 year ago

good first issue

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Add cramino for uBAM input about 1 year ago

enhancement good first issue Gain M Effort S Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Add Abacus as an STR expansion caller about 1 year ago

enhancement good first issue Gain L Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Add mitochondrial-specific calling about 1 year ago

enhancement good first issue

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

Remove or replace cramino with nf-core module about 1 year ago

good first issue Gain M Effort M Urgency M

genomic-medicine-sweden/nallo

68

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Nextflow

#gms#long-read-sequencing#nanopore#pacbio#variant-calling

genomic-medicine-sweden/nallo

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