RKIBioinformaticsPipelines/ncov_minipipe issues and pull requests

#128 - NameError: name 'conda_frontend' is not defined

Issue - State: closed - Opened by siligam over 2 years ago - 2 comments

#127 - SARS-CoV-2 workflow comparison - kindly check if you work is represented correctly

Issue - State: opened - Opened by thomasbtf over 2 years ago - 2 comments

#126 - 3.1.0 on DockerHub?

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

#125 - plot too large

Issue - State: opened - Opened by oliverdrechsel almost 3 years ago

#124 - update krakenDB

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

#123 - adjust README - install with mamba

Issue - State: closed - Opened by oliverdrechsel almost 3 years ago

#122 - add president rule

Issue - State: opened - Opened by MarieLataretu almost 3 years ago
Labels: improvement

#121 - document difference between --var_call_frac and --gt_adjust

Issue - State: opened - Opened by MarieLataretu almost 3 years ago
Labels: documentation

#119 - Error in filterVarsConsensus

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

#118 - Error in rule createReport

Issue - State: closed - Opened by MarieLataretu about 3 years ago - 1 comment
Labels: Bug

#117 - install method 2.2.2 does not work

Issue - State: closed - Opened by oliverdrechsel about 3 years ago - 1 comment

#116 - Current Version (3.0.5) no longer compatible with latest pangolin version

Issue - State: closed - Opened by alex-seitz over 3 years ago - 2 comments
Labels: Bug

#115 - Automatically detect and report a minimal set of primer pairs to "repair" a genome

Issue - State: opened - Opened by hoelzer over 3 years ago

#114 - Consensus Issue with ambiguous called variants.

Issue - State: opened - Opened by benwulf over 3 years ago - 3 comments
Labels: open question

#113 - Nimagen assay 114 with 150BP reads

Issue - State: opened - Opened by benwulf over 3 years ago
Labels: improvement

#112 - No latest tag on dockerhub

Issue - State: opened - Opened by fabianrost over 3 years ago - 1 comment

#111 - Generate summary heatmap of variants per run

Issue - State: opened - Opened by hoelzer over 3 years ago
Labels: improvement

#110 - sortable tables in qc_report.html

Issue - State: opened - Opened by fabianrost over 3 years ago - 3 comments

#109 - Error in rule annotateVariants with custom annotation

Issue - State: opened - Opened by fabianrost over 3 years ago - 4 comments
Labels: improvement

#108 - reduce file size docker image

Issue - State: opened - Opened by fabianrost over 3 years ago - 3 comments

#107 - making docker container usable with singularity

Issue - State: closed - Opened by fabianrost over 3 years ago - 3 comments
Labels: improvement

#106 - quicktest fails after fresh quick setup

Issue - State: closed - Opened by fabianrost over 3 years ago - 1 comment

#105 - put annotations of genome into separate folder

Issue - State: opened - Opened by oliverdrechsel over 3 years ago

#104 - automatically check for new versions of the pipeline at each start

Issue - State: closed - Opened by oliverdrechsel over 3 years ago

#103 - Allow shorter reads

Issue - State: closed - Opened by bwlang over 3 years ago - 5 comments
Labels: improvement

#102 - update to Snakemake 6.x.x. ?

Issue - State: closed - Opened by oliverdrechsel over 3 years ago - 1 comment

#101 - QC-metrics for upload to RKI

Issue - State: opened - Opened by alex-seitz over 3 years ago - 3 comments
Labels: improvement

#100 - Error on fastq-files with no input

Issue - State: closed - Opened by alex-seitz over 3 years ago - 3 comments
Labels: Bug, high priority

#99 - CoVpipe version in output files

Issue - State: closed - Opened by regelkamp over 3 years ago - 1 comment
Labels: Bug, Doing, medium priority

#98 - fuse lineage output into one file

Issue - State: closed - Opened by oliverdrechsel over 3 years ago - 1 comment
Labels: improvement

#97 - Validation samples

Issue - State: closed - Opened by gabeng over 3 years ago - 2 comments

#96 - Potential variant filtering issue results in misclassification of B.1.1.7 positive sample

Issue - State: closed - Opened by mbeckste over 3 years ago - 3 comments
Labels: Done

#95 - include variants of interest in report

Issue - State: closed - Opened by oliverdrechsel over 3 years ago
Labels: high priority, improvement

#94 - fragment length filter + read length filter (as paramter)

Issue - State: opened - Opened by oliverdrechsel over 3 years ago - 1 comment
Labels: improvement

#93 - PHRED read quality 20 instead of 15

Issue - State: closed - Opened by oliverdrechsel over 3 years ago

#92 - adapter.fasta given in parameter is not entered in config file

Issue - State: closed - Opened by oliverdrechsel over 3 years ago - 1 comment
Labels: Bug, high priority

#91 - Automate Docker image build

Issue - State: opened - Opened by hoelzer over 3 years ago - 3 comments
Labels: improvement, medium priority

#90 - Error while building docker

Issue - State: opened - Opened by nicolegruenheit over 3 years ago - 8 comments

#89 - warn, if frameshift mutations were incorporated into consensus sequence

Issue - State: opened - Opened by oliverdrechsel over 3 years ago
Labels: improvement, medium priority

#88 - unrecognized arguments: --threads for Pangolin

Issue - State: closed - Opened by SrPeter128 over 3 years ago - 4 comments

#87 - Error in rule annotateAmbiguousConsensus

Issue - State: closed - Opened by fabianrost over 3 years ago - 6 comments
Labels: Bug, To Do

#86 - CondaVerificationError: dos2unix

Issue - State: closed - Opened by fabianrost over 3 years ago - 3 comments
Labels: Bug

#85 - README mentions unsupported --krakenDb

Issue - State: closed - Opened by fabianrost over 3 years ago - 2 comments
Labels: To Do, improvement

#84 - Variant B.1.1.7 not detected with CoVpipe

Issue - State: closed - Opened by titochungo over 3 years ago - 26 comments
Labels: To Do, high priority

#83 - quicktest error with sam file

Issue - State: closed - Opened by alex-seitz almost 4 years ago - 5 comments
Labels: Done

#82 - ncov_minipipe crashes with TypeError: sequence item 0: expected str instance, NoneType found

Issue - State: closed - Opened by fabianrost almost 4 years ago - 2 comments
Labels: Bug, Doing

#81 - quicktest fails upon realpath

Issue - State: closed - Opened by fabianrost almost 4 years ago - 2 comments
Labels: Done

#80 - quicktest fails to find activate after `conda activate covpipe`

Issue - State: closed - Opened by fabianrost almost 4 years ago - 1 comment
Labels: Done

#79 - Update the pipeline

Issue - State: opened - Opened by hoelzer almost 4 years ago - 1 comment
Labels: improvement, usability

#78 - Add pip install to readme

Issue - State: closed - Opened by rekm almost 4 years ago

#77 - Add consensus QC script to the pipeline

Issue - State: opened - Opened by hoelzer almost 4 years ago
Labels: improvement, low priority

#76 - Masked consensus and other fastas do not end with a newline

Issue - State: closed - Opened by rekm almost 4 years ago
Labels: Done

#75 - htmltools error when knitting the report

Issue - State: closed - Opened by rekm almost 4 years ago
Labels: Doing

#74 - take mulitple fasta entries into account

Issue - State: opened - Opened by oliverdrechsel almost 4 years ago
Labels: improvement, medium priority

#73 - Additional python dependencies for `create_bedpe.py`

Issue - State: closed - Opened by hoelzer almost 4 years ago - 1 comment
Labels: improvement, info, usability

#72 - check map2 genome ratio

Issue - State: opened - Opened by oliverdrechsel almost 4 years ago
Labels: low priority

#71 - report human read count in classification

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago

#70 - check amplicon coverage for report

Issue - State: opened - Opened by oliverdrechsel almost 4 years ago - 1 comment
Labels: improvement, low priority

#69 - highlight clade defining variants in report

Issue - State: opened - Opened by oliverdrechsel almost 4 years ago
Labels: improvement, low priority

#68 - make report more robust to large plots/sample counts

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago

#67 - remove trailing \n in masked sequences

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: Done

#66 - add option to retreive reference directly from NCBI by ID

Issue - State: opened - Opened by oliverdrechsel almost 4 years ago
Labels: Doing

#65 - Tag positive and negative sample list with reference coverage

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: Done

#64 - put wrapper logs to rules/log folder

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: Doing, low priority, usability

#63 - does annotate SNPs work?

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: Done, high priority

#62 - ./results/intermediate/03* is missing

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: improvement, low priority

#61 - Revise adjust_gt.py

Issue - State: closed - Opened by hoelzer almost 4 years ago
Labels: code hygiene, low priority, usability

#60 - Genome name is hard-coded in inspect variants rule

Issue - State: closed - Opened by hoelzer almost 4 years ago - 1 comment
Labels: low priority, usability

#59 - Script paths only work with wrapper and not with direct execution via snakefile

Issue - State: closed - Opened by hoelzer almost 4 years ago - 2 comments
Labels: usability

#58 - pipeline gets into undefined state, if not a git repo

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: Bug, high priority

#57 - check, if conda setup works without .git folder

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: high priority

#56 - snakemake reruns all rules in wrapper context

Issue - State: closed - Opened by oliverdrechsel almost 4 years ago
Labels: improvement, low priority

#55 - Create report rule fails for test data

Issue - State: closed - Opened by hoelzer almost 4 years ago - 1 comment
Labels: Bug, Done

#52 - make amplicon cleaning optional again

Issue - State: closed - Opened by oliverdrechsel about 4 years ago

#51 - move config[] calls into global variables

Issue - State: closed - Opened by oliverdrechsel about 4 years ago
Labels: code hygiene, medium priority

#50 - test how bcftools creates consensus on mixed variants

Issue - State: closed - Opened by oliverdrechsel about 4 years ago

#49 - create fastq with mixed variant

Issue - State: closed - Opened by oliverdrechsel about 4 years ago

#47 - reduce storage footprint of pipeline

Issue - State: closed - Opened by oliverdrechsel about 4 years ago

#46 - move filter paramters into config

Issue - State: closed - Opened by oliverdrechsel about 4 years ago - 2 comments
Labels: code hygiene, improvement

#45 - kraken database on zendoo has wrong name

Issue - State: closed - Opened by hoelzer about 4 years ago - 1 comment
Labels: low priority, usability

#44 - split snake rules into smaller files

Issue - State: closed - Opened by oliverdrechsel about 4 years ago
Labels: improvement, low priority

#43 - cutadapt - check linked adapters

Issue - State: closed - Opened by oliverdrechsel about 4 years ago
Labels: improvement, medium priority

#42 - include GATK VariantEval

Issue - State: opened - Opened by oliverdrechsel about 4 years ago
Labels: improvement, low priority

#41 - projfolder as constant (upper letters)

Issue - State: closed - Opened by s.fuchs about 4 years ago
Labels: code hygiene, low priority

#40 - provide a config file template

Issue - State: closed - Opened by s.fuchs about 4 years ago
Labels: low priority, usability

#39 - individual rule files

Issue - State: closed - Opened by s.fuchs about 4 years ago
Labels: code hygiene, medium priority

#37 - Swap GATK by loFreq or iVar

Issue - State: closed - Opened by oliverdrechsel about 4 years ago - 1 comment
Labels: high priority, improvement

#36 - Provide tiny test data for cleanplex

Issue - State: closed - Opened by s.fuchs about 4 years ago - 1 comment
Labels: high priority, testing

#34 - Snakemake 5.23.0 to Snakemake 5.25.0-1 are broken

Issue - State: closed - Opened by rekm about 4 years ago - 2 comments
Labels: info, waiting

#32 - reduce memory footprint of QC report

Issue - State: closed - Opened by oliverdrechsel about 4 years ago
Labels: improvement, medium priority

#31 - switch multi sample to single sample calling

Issue - State: closed - Opened by oliverdrechsel about 4 years ago - 1 comment
Labels: high priority

#30 - use --keep-intermediate-files switch to keep temp() files in snakemake

Issue - State: closed - Opened by oliverdrechsel about 4 years ago - 1 comment
Labels: To Do, improvement, low priority

#29 - optional: export tables from QCreport as csv

Issue - State: closed - Opened by oliverdrechsel about 4 years ago
Labels: improvement, low priority

#28 - Make tables in QC sortable and searchable

Issue - State: opened - Opened by oliverdrechsel about 4 years ago
Labels: low priority, usability

#27 - InDels modify sequence length before N masking

Issue - State: closed - Opened by oliverdrechsel about 4 years ago - 1 comment
Labels: Bug, high priority

#26 - Tests: Low Coverage Tests

Issue - State: opened - Opened by rekm about 4 years ago
Labels: medium priority, testing

#25 - Dealing with duplicate sample ids

Issue - State: closed - Opened by rekm about 4 years ago
Labels: Bug, high priority

#24 - offer script dealing with conda startup

Issue - State: closed - Opened by rekm about 4 years ago - 1 comment
Labels: Done, low priority, usability

#23 - Snakemake call returned non zero exit status

Issue - State: closed - Opened by xlinxlin over 4 years ago - 2 comments

#1 - generate mapping rule

Issue - State: closed - Opened by oliverdrechsel over 4 years ago

GitLab.com / RKIBioinformaticsPipelines/ncov_minipipe issues and pull requests