Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/viralrecon issues and pull requests

#403 - Unable to download the python script

Issue - State: open - Opened by Mahendra687 about 1 year ago
Labels: bug

#401 - Added option to add a custom annotation

Pull Request - State: open - Opened by svarona about 1 year ago - 1 comment

#400 - Adding "aggregate" and "plot" methods in the freyja subworkflow

Issue - State: open - Opened by bsalehe about 1 year ago
Labels: enhancement

#399 - Problem installing viralrecon

Issue - State: open - Opened by vilocha about 1 year ago
Labels: bug

#397 - Important! Template update for nf-core/tools v2.10

Pull Request - State: open - Opened by nf-core-bot about 1 year ago

#396 - Apply samtools fixmate after ivar trim

Pull Request - State: open - Opened by wutron about 1 year ago - 1 comment

#395 - Remove minia from default assembler

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 2 comments

#393 - Changed primer set to params

Pull Request - State: open - Opened by svarona over 1 year ago - 2 comments

#391 - primer_set is not taking param

Issue - State: open - Opened by svarona over 1 year ago
Labels: bug

#390 - Allow viralrecon to take gtf as input annotation file

Issue - State: open - Opened by svarona over 1 year ago
Labels: enhancement

#389 - epi2me-labs/wf-cnv failed during analysis

Issue - State: closed - Opened by Ligerd5 over 1 year ago - 7 comments

#388 - adding fastqc trimmed in report

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago - 2 comments

#387 - Remove system exit 1

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 1 comment

#386 - Raise error instead of system.exit(1)

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 1 comment

#385 - [bug] Fails to find FASTQ files when stored on S3

Issue - State: open - Opened by adamrtalbot over 1 year ago
Labels: bug

#384 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 2 comments

#382 - Minimum frequency threshold is being ignored

Issue - State: open - Opened by AndreaAguadoM over 1 year ago - 1 comment
Labels: bug

#381 - Minia assembly is non-deterministic in parallel

Issue - State: open - Opened by tetedange13 over 1 year ago - 1 comment
Labels: enhancement

#380 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#378 - Suggestions regarding BLAST step

Issue - State: open - Opened by tetedange13 over 1 year ago
Labels: enhancement

#377 - Feat/implement nf tests

Pull Request - State: closed - Opened by sateeshperi over 1 year ago - 1 comment
Labels: WIP

#375 - Adding new nf-core subworkflow freyja for weighted variant analysis

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago - 3 comments
Labels: enhancement, subworkflows

#374 - Custom .yaml and .txt for MultiQC and pangolin/nextclade version changes (-c error)

Issue - State: closed - Opened by rarthur-eicc over 1 year ago - 1 comment
Labels: bug

#373 - Add support for artic primer set version V5.3.2

Issue - State: open - Opened by mbdabrowska1 over 1 year ago - 11 comments
Labels: enhancement

#372 - Bump pipeline version to 2.7.0dev

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 1 comment

#371 - Add subworkflows to nf-core

Issue - State: open - Opened by drpatelh over 1 year ago
Labels: enhancement, subworkflows, new subworkflow

#370 - Fix #368

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 7 comments

#369 - Missing conda package for ivar_variants_to_vcf.nf

Issue - State: closed - Opened by wutron over 1 year ago - 2 comments
Labels: bug

#368 - Incorrect depth from ivar variants reported in variants long table

Issue - State: closed - Opened by wutron over 1 year ago - 2 comments
Labels: bug

#367 - ADD Subway map

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 5 comments

#366 - Final pre-release fixes

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 2 comments

#365 - Create new folder on test-datasets for all samplesheets

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 1 comment

#364 - Remove native processes using local executor

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 1 comment

#363 - Aws paths

Pull Request - State: closed - Opened by FriederikeHanssen over 1 year ago - 1 comment

#362 - Bump pipeline version and other pre-release fixes

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 1 comment

#361 - Dev -> Master for 2.6 release

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 2 comments

#360 - Fix #316 #320 #349

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 1 comment

#359 - Update modules/subworkflows to latest syntax

Pull Request - State: closed - Opened by drpatelh over 1 year ago - 2 comments

#358 - Wrap params string in file method

Pull Request - State: closed - Opened by robsyme over 1 year ago - 7 comments

#357 - AWS Access Key Id you provided does not exist in our records

Issue - State: closed - Opened by anca-riza almost 3 years ago - 1 comment

#356 - NEB SARS-CoV-2 primers

Issue - State: closed - Opened by tavareshugo almost 2 years ago - 3 comments

#355 - MERGE TEMPLATE

Pull Request - State: closed - Opened by maxulysse almost 2 years ago - 3 comments

#354 - Error "No PSK available. Unable to resume."

Issue - State: closed - Opened by forty2wallabyway almost 2 years ago - 2 comments
Labels: bug

#353 - Adding support for Atoplex kit

Issue - State: closed - Opened by ctuni almost 2 years ago - 3 comments
Labels: enhancement

#352 - Joon klaps/issue351

Pull Request - State: closed - Opened by Joon-Klaps almost 2 years ago - 1 comment

#351 - Outdated module folder structure

Issue - State: closed - Opened by Joon-Klaps almost 2 years ago
Labels: enhancement

#350 - Choose Kraken2-filtered host

Issue - State: open - Opened by tetedange13 almost 2 years ago - 3 comments
Labels: enhancement

#349 - ERROR in Script plasmidID

Issue - State: closed - Opened by AroobAlhumaidy almost 2 years ago - 1 comment
Labels: bug

#348 - [DOC] Document full parameters of iVar consensus

Issue - State: closed - Opened by corneliusroemer almost 2 years ago - 2 comments

#347 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago

#346 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#345 - multiqc error using dev branch

Issue - State: open - Opened by rrdavis77 almost 2 years ago - 9 comments
Labels: WIP, bug

#344 - Update bowtie2 related modules and subworkflows

Pull Request - State: closed - Opened by maxulysse almost 2 years ago - 2 comments

#343 - Bump artic

Pull Request - State: closed - Opened by tavareshugo almost 2 years ago - 3 comments

#342 - fix merge TEMPLATE

Pull Request - State: closed - Opened by maxulysse almost 2 years ago - 5 comments

#341 - Latest medaka models not available - update artic module

Issue - State: closed - Opened by tavareshugo almost 2 years ago - 8 comments
Labels: bug

#340 - Mac

Pull Request - State: closed - Opened by Joon-Klaps about 2 years ago - 1 comment

#339 - Exit code 255 when running MAKE_VARIANTS_LONG_TABLE process for the test dataset

Issue - State: closed - Opened by mbdabrowska1 about 2 years ago - 5 comments
Labels: bug

#338 - Pipeline reports mapped reads as 'NA' even tough viral genome aligning reads are present

Issue - State: closed - Opened by leiendeckerlu about 2 years ago - 1 comment
Labels: bug

#337 - ivar_variants_to_vcf.py collapses low quality ivar variant with high quality variant

Issue - State: open - Opened by Rohit-Satyam about 2 years ago - 4 comments
Labels: bug

#336 - Clarify documentation on variants tables (inconsistent between platforms)

Issue - State: open - Opened by tavareshugo about 2 years ago - 1 comment
Labels: enhancement

#335 - The ivar_variants_to_vcf.py does not sort variant

Issue - State: closed - Opened by Rohit-Satyam about 2 years ago - 4 comments
Labels: bug

#334 - Longshot thread 'main' panicked at 'assertion failed: p <= 0.0' error

Issue - State: closed - Opened by ddomman about 2 years ago - 1 comment
Labels: bug

#333 - Cutadapt error with -profile test,singularity

Issue - State: closed - Opened by tetedange13 about 2 years ago - 4 comments
Labels: bug

#332 - Add support for MGI's Atoplex kit

Issue - State: closed - Opened by ljmesi about 2 years ago - 2 comments
Labels: enhancement

#331 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago

#330 - Update V1200 primer scheme

Issue - State: open - Opened by ddomman about 2 years ago - 1 comment
Labels: enhancement

#329 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#328 - Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:BCFTOOLS_SORT

Issue - State: closed - Opened by Rooksie about 2 years ago - 3 comments
Labels: bug

#327 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#326 - Fixed ivar_variants_to_vcf.py exception

Pull Request - State: closed - Opened by mattheww95 over 2 years ago - 5 comments

#325 - Fixed problem with no annotation and duplicated lines in ivar_variants_to_vcf_script

Pull Request - State: closed - Opened by saramonzon over 2 years ago - 1 comment

#324 - Issues pulling singularity images

Issue - State: closed - Opened by Aqsakhalid30 over 2 years ago - 3 comments
Labels: bug

#323 - Patch 2

Pull Request - State: closed - Opened by tavareshugo over 2 years ago - 1 comment

#322 - Error in the last 2 steps

Issue - State: closed - Opened by Yelbur over 2 years ago - 2 comments
Labels: bug

#321 - Custom GFF file failing ivar_variants_to_vcf.py with release 2.5

Issue - State: closed - Opened by afonsoguerra over 2 years ago - 9 comments
Labels: bug

#320 - Pipeline fails at email step: Failed to invoke workflow.onComplete event handler

Issue - State: closed - Opened by rarthur-eicc over 2 years ago - 6 comments
Labels: bug

#319 - Bump pipeline version to 2.6dev

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#318 - Fix #316

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#317 - Enable --ignore_merge_codons in ivar_variants_to_vcf when no .gff file is given

Issue - State: closed - Opened by svarona over 2 years ago
Labels: enhancement

#316 - Variant calling isn't run when using --skip_asciigenome with metagenomic data

Issue - State: closed - Opened by svarona over 2 years ago - 3 comments
Labels: bug

#315 - Dev -> Master for 2.5 release

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 2 comments

#314 - Update modules and fix bugs for v2.5 release

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#313 - update conda recipe for artic minion

Pull Request - State: closed - Opened by tavareshugo over 2 years ago - 6 comments

#312 - broken redirect for medaka model

Issue - State: closed - Opened by alethomas over 2 years ago - 1 comment
Labels: bug

#311 - Invalid declaration `val medaka_model_string`

Issue - State: closed - Opened by alethomas over 2 years ago - 1 comment
Labels: bug

#310 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#307 - Replace vanilla Linux Biocontainer with Ubuntu

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#306 - Add contig field information in vcf header in ivar_variants_to_vcf and use bcftools sort

Issue - State: closed - Opened by saramonzon over 2 years ago - 3 comments
Labels: enhancement

#305 - single barcode

Issue - State: closed - Opened by Mewgia over 2 years ago - 1 comment

#304 - Re-factor code for ivar_variants_to_vcf script

Pull Request - State: closed - Opened by saramonzon over 2 years ago - 2 comments