iobis/PacMAN-pipeline issues and pull requests

#94 - make_dwca: argument is of length zero

Issue - State: closed - Opened by pieterprovoost 11 months ago
Labels: bug

#93 - dada2_ASV: Tibble columns must have compatible sizes.

Issue - State: closed - Opened by pieterprovoost 11 months ago - 1 comment
Labels: bug

#92 - Ensure that original identification is preserved regardless of WoRMS match

Issue - State: open - Opened by pieterprovoost 11 months ago
Labels: WoRMS matching

#91 - Add citation

Issue - State: open - Opened by pieterprovoost 12 months ago

#90 - Incorrect assignments in Everglades 12S

Issue - State: closed - Opened by pieterprovoost 12 months ago - 1 comment
Labels: bug

#89 - Improve occurrenceID naming

Issue - State: open - Opened by pieterprovoost about 1 year ago

#88 - Fixes to taxonomy parsing in get-lsids

Pull Request - State: closed - Opened by pieterprovoost about 1 year ago

#87 - High level RDP classification despite good BLAST hits

Issue - State: open - Opened by pieterprovoost about 1 year ago

#86 - Handle taxonomy strings from BLAST

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

#85 - Some DNADerivedData fields not exported

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

#84 - Dada2_ASVInference_Single: object 'abundance' not found

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

#83 - Write tests for taxonomic annotation

Issue - State: open - Opened by pieterprovoost about 1 year ago
Labels: WoRMS matching

#82 - Vsearch hits and identities not properly included in compare_taxa

Issue - State: closed - Opened by pieterprovoost about 1 year ago - 1 comment
Labels: bug

#81 - BLCA does not handle nan in taxonomy

Issue - State: closed - Opened by pieterprovoost over 1 year ago
Labels: blca

#80 - Detect prefixed taxonomy strings

Issue - State: closed - Opened by pieterprovoost over 1 year ago

#79 - Add taxonomy confidence levels to DwC

Issue - State: closed - Opened by pieterprovoost over 1 year ago - 1 comment
Labels: blca

#78 - Fix for missing votes in BLCA

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

#77 - BLCA: ValueError: max() arg is an empty sequence

Issue - State: closed - Opened by pieterprovoost over 1 year ago
Labels: bug, blca

#76 - Rename blca_identity_cutoff

Issue - State: closed - Opened by pieterprovoost over 1 year ago - 1 comment
Labels: blca

#75 - Taxon matching improvements

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

#74 - Make results path configurable

Issue - State: open - Opened by pieterprovoost over 1 year ago

#73 - Taxon matching stops silently with (429) Too Many Requests

Issue - State: open - Opened by pieterprovoost over 1 year ago - 1 comment
Labels: bug, WoRMS matching

#72 - Add clean taxonomy and scientific name

Issue - State: closed - Opened by pieterprovoost over 1 year ago
Labels: WoRMS matching

#71 - Incomplete taxon matching

Issue - State: open - Opened by pieterprovoost over 1 year ago
Labels: bug, WoRMS matching

#70 - Remove nan values from occurrence table

Issue - State: open - Opened by pieterprovoost over 1 year ago

#69 - Change DwC-A file extensions to tsv or txt

Issue - State: closed - Opened by pieterprovoost over 1 year ago

#68 - AlignIO: No records found in handle

Issue - State: closed - Opened by pieterprovoost over 1 year ago
Labels: bug

#67 - Sample IDs in report from sample metadata instead of manifest

Issue - State: closed - Opened by pieterprovoost over 1 year ago

#66 - Report fails due to absolute path for sample data

Issue - State: closed - Opened by pieterprovoost over 1 year ago
Labels: bug

#65 - Add instructions for downloading NCBI nt

Issue - State: open - Opened by pieterprovoost over 1 year ago
Labels: documentation

#64 - blastn: Out of memory

Issue - State: open - Opened by pieterprovoost over 1 year ago - 2 comments
Labels: bug

#63 - fix for no single reads after dada2 filtering

Pull Request - State: closed - Opened by SSuominen1 almost 2 years ago

#62 - Bugs

Pull Request - State: closed - Opened by SSuominen1 almost 2 years ago

#61 - Fix cutadapt finish all files before dada2

Pull Request - State: closed - Opened by SSuominen1 almost 2 years ago - 1 comment

#60 - dada2_filter: Error in files_exist[[i]]: subscript out of bounds

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#59 - dada2_filter fails on missing unpaired cutadapt files

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#58 - Incorrect taxonomy statistics in report

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#57 - dada2_filter failing on missing cutadapt_unpaired output files

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#56 - Report barcharts not readable in case of many samples

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: bug

#55 - Bowtie2 and Cutadapt not available for Windows

Issue - State: closed - Opened by pieterprovoost about 2 years ago - 1 comment

#54 - No sequences left after chimera removal?

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#53 - Rule make_dwca: invalid class “phyloseq” object

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#52 - Why is mergePairs with returnRejects = FALSE returning short (200) sequences?

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: dataset: rey

#51 - Key 120 (char 'x') not in lookup table

Issue - State: closed - Opened by pieterprovoost about 2 years ago - 1 comment
Labels: bug, duplicate, dataset: rey

#50 - Issue in dada2_asv for file sets of size 1

Issue - State: closed - Opened by pieterprovoost about 2 years ago - 1 comment
Labels: bug, dataset: rey

#49 - Pipeline fails with larger set of files

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#48 - Add taxonomy fields

Pull Request - State: closed - Opened by pieterprovoost about 2 years ago

#47 - Map reads to ASVs

Pull Request - State: closed - Opened by pieterprovoost about 2 years ago

#46 - Pipeline fails with BLAST include = False

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug

#45 - Anthomyiidae sp. BOLD_ACC9466 mapped to urn:lsid:marinespecies.org:taxname:1

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: bug, WoRMS matching

#44 - Add specificEpithet and taxonRank in occurrence table

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: WoRMS matching

#43 - Some results have kingdom and scientificName = Unknown

Issue - State: open - Opened by pieterprovoost about 2 years ago
Labels: bug, dataset: rey

#42 - dada2_ASV: Error in getUniques(x) : Unrecognized format

Issue - State: closed - Opened by pieterprovoost about 2 years ago - 3 comments
Labels: bug, dataset: rey

#41 - Error in rule reporting

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

#40 - IO error: ncbi/taxonomy/complete_taxa.db/LOCK: Permission denied

Issue - State: closed - Opened by pieterprovoost about 2 years ago
Labels: bug

#39 - Use period for decimal separator

Issue - State: closed - Opened by pieterprovoost over 2 years ago - 1 comment
Labels: bug, wontfix, Darwin Core

#38 - Remove NA values from CSV output

Issue - State: closed - Opened by pieterprovoost over 2 years ago
Labels: bug, Darwin Core

#37 - Reading yaml in report fails

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

#36 - multiqc: ImportError: cannot import name 'Protocol'

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

#35 - Upgraded biostrings and dada2

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

#34 - R package conflicts

Issue - State: closed - Opened by pieterprovoost over 2 years ago
Labels: bug, wontfix

#33 - Workflow breaks when --configfile is not provided

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

#32 - configfile parameter name

Issue - State: closed - Opened by pieterprovoost over 2 years ago

#16 - Fixes

Pull Request - State: closed - Opened by SSuominen1 almost 3 years ago

#15 - Fixes

Pull Request - State: closed - Opened by SSuominen1 about 3 years ago