nf-core/metatdenovo issues and pull requests

#208 - Updated modules to use the latest tidyverse env

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

#207 - Different versions of R container

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

#206 - Update usage.md

Pull Request - State: open - Opened by erikrikarddaniel about 1 year ago - 2 comments

#205 - Output.md updates

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

#204 - It would be nice with counts for annotations in overall stats

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

#203 - Fix single end

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

#202 - Fix eukulele

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

#201 - Eukulele duplicates, and other Eukulele small bugs

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

#200 - Update modules

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

#199 - multiqc report printed in results/multiqc

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

#198 - MultiQC report in the wrong directory?

Issue - State: closed - Opened by erikrikarddaniel about 1 year ago - 2 comments
Labels: bug

#197 - Update documentation

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

#196 - Fix eggnog download no copy ode

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

#195 - changed the way eggnog download works

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

#194 - Fix small issues

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

#193 - Fix issue 183 eukulele user name

Pull Request - State: closed - Opened by danilodileo about 1 year ago - 3 comments

#192 - Deal properly with download of data

Issue - State: closed - Opened by danilodileo about 1 year ago - 2 comments
Labels: enhancement

#191 - Issue 168 deal properly with download of data

Pull Request - State: closed - Opened by tfalkarkea about 1 year ago - 3 comments

#190 - Eukulele download module removed

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

#188 - Template update 2.10

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

#187 - Template merge 2.10

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

#186 - Output concatenated ffn files from Prokka

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

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

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

#184 - Listing db-versions in output-file/multiqc-report

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

#183 - when using EUKulele user's database error name output

Issue - State: closed - Opened by danilodileo about 1 year ago - 3 comments
Labels: bug

#182 - BBNORM: Cannot run program “bgzip”

Issue - State: closed - Opened by BenPonBiobrain about 1 year ago - 2 comments
Labels: bug

#181 - Contig length filter

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

#180 - Fix prefix for eukulele columns in summary

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

#179 - Assembly and orf caller prefix in column name should not be there

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

#178 - Fix filenames

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

#177 - Mix of filenames specified in modules.config and module code

Issue - State: open - Opened by erikrikarddaniel about 1 year ago
Labels: question

#176 - Eukulele works poorly with `-resume`

Issue - State: closed - Opened by erikrikarddaniel about 1 year ago - 3 comments
Labels: bug

#175 - Prokka gff2tsv

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

#174 - Update local modules to new container syntax + more

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

#173 - Format prodigal module update

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

#172 - added input single_end option

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

#171 - (At least) GTDB fails to download

Issue - State: open - Opened by erikrikarddaniel over 1 year ago - 4 comments
Labels: bug

#170 - Parameter value check(s) doesn't work

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

#169 - `SUM_TAXONOMY` and other summary modules produces empty output with RNASpades/Prodigal

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 3 comments
Labels: bug

#168 - Deal properly with download of data

Issue - State: closed - Opened by maxulysse over 1 year ago - 9 comments
Labels: bug

#167 - Issue 162 add assembler qc report

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

#166 - Cosmetics: `EUKULELE_DOWNLOAD` reports `$meta.id`

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

#165 - Warning messages we should deal with

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

#164 - TSV table from Prokka GFF

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 1 comment
Labels: enhancement

#163 - Get a name for MultiQC based on combination of assembler and ORF caller

Issue - State: closed - Opened by danilodileo over 1 year ago - 2 comments
Labels: enhancement

#162 - Add assembler QC report

Issue - State: closed - Opened by tfalkarkea over 1 year ago - 6 comments
Labels: enhancement

#161 - fix aesthetic

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

#160 - Remove diginorm

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

#159 - Update modules

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

#158 - wrong meta.id defined in prodigal

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

#157 - Template 2.9

Pull Request - State: closed - Opened by danilodileo over 1 year ago - 4 comments

#156 - remove diginorm

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#155 - Fix kofam issues

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

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

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

#153 - Clean eukulele search module

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

#152 - sample name can be a number or a character and it will not crush at c…

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

#151 - `merge_tables` and `collect_stats` fails if sample names are just digits

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

#150 - Clean up Eukulele search module

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

#149 - EUKULELE/GTDB summary tables

Issue - State: closed - Opened by BenPonBiobrain over 1 year ago - 3 comments
Labels: bug

#148 - Eukulele/GTDB: We're one rank off

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

#147 - ---

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

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

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

#145 - Gzip files

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

#144 - check all saved files

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#143 - Is `param.kofam_dir` not used?

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 4 comments
Labels: bug

#142 - kofamscan needs to be part of the summary

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#141 - Merge tables bug

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

#140 - Make kofamscan use all cpus

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

#139 - unzip file

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

#138 - kofamscan gets gzipped file from prodigal that it can't handle

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

#137 - Use barrnap to filter reads

Issue - State: open - Opened by erikrikarddaniel over 1 year ago - 3 comments
Labels: enhancement

#136 - Samtools sort updata

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

#135 - Remove warnings

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

#134 - Parameters upadate

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

#133 - add CITATIONS + moved orf caller right after the assembly step

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

#132 - Move gene calling code higher up

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 1 comment
Labels: enhancement

#131 - update citations.md

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#130 - Spelling things

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

#129 - Gzip all tables in `summary_tables`

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 1 comment
Labels: enhancement

#128 - Readme update

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

#127 - Update modules

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

#126 - updated usage.md

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

#125 - Check main workflow before the release

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

#124 - update usage.md

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#123 - update parameters section

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#122 - How does the nf-core offline tool work, can we use it to pre-download databases?

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 1 comment
Labels: enhancement

#121 - update README.md

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#120 - update metatdenovo diagram

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

#119 - update nf-core modules

Issue - State: closed - Opened by danilodileo over 1 year ago - 1 comment
Labels: enhancement

#118 - Fix kofamscan download output

Pull Request - State: closed - Opened by danilodileo over 1 year ago - 4 comments

#117 - schema.json updated

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

#116 - Fix file arguments in `nextflow_schema.json`

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 2 comments
Labels: enhancement

#115 - Bbmap bbnorm

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

#114 - Kofamscan

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

#113 - Fix merge table

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

#112 - fix sum_taxonomy.nf error

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

#111 - GTDB taxonomy for CAT

Issue - State: closed - Opened by erikrikarddaniel over 1 year ago - 3 comments
Labels: enhancement

#110 - added meta.id to output

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

#109 - Add new programs to MULTIQC

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

#108 - Update documentation

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

GitHub / nf-core/metatdenovo issues and pull requests