Ecosyste.ms: Issues

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

GitHub / nf-core/kmermaid issues and pull requests

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

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

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

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

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

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

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

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

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

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

#152 - Fixes to run in July 2022

Pull Request - State: open - Opened by olgabot over 2 years ago

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

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

#150 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#149 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#147 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 2 comments

#146 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot about 3 years ago - 1 comment

#145 - Important! Template update for nf-core/tools v2.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#144 - Important! Template update for nf-core/tools v2.0.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#143 - Important! Template update for nf-core/tools v2.0

Pull Request - State: closed - Opened by KevinMenden over 3 years ago - 1 comment

#142 - Important! Template update for nf-core/tools v1.14

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago - 1 comment

#141 - Pipeline has 2 releases, but default branch is dev

Issue - State: open - Opened by maxulysse almost 4 years ago
Labels: bug

#140 - Add --singleton option for sourmash

Pull Request - State: open - Opened by olgabot almost 4 years ago

#139 - TEMPLATE needs cleaning

Issue - State: open - Opened by ewels almost 4 years ago
Labels: bug

#138 - Important! Template update for nf-core/tools v1.13.2

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago - 2 comments

#137 - Important! Template update for nf-core/tools v1.13.1

Pull Request - State: closed - Opened by KevinMenden almost 4 years ago - 1 comment

#136 - Important! Template update for nf-core/tools v1.13

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago

#135 - Add sourmash search

Pull Request - State: open - Opened by olgabot almost 4 years ago

#134 - Add hash2kmer.py code to get potential genes and sequences for each k-mer hash

Issue - State: open - Opened by olgabot almost 4 years ago
Labels: enhancement

#133 - KMERMAID: Convert all parameter docs to JSON schema

Issue - State: open - Opened by apeltzer almost 4 years ago - 1 comment
Labels: enhancement

#132 - olgabot/sourmash sig merge v2

Pull Request - State: closed - Opened by olgabot almost 4 years ago - 1 comment

#131 - Remove constitutive k-mers

Pull Request - State: open - Opened by olgabot almost 4 years ago

#130 - Update to sourmash 4.0

Issue - State: open - Opened by olgabot almost 4 years ago
Labels: enhancement

#129 - Output fastas for translate

Pull Request - State: closed - Opened by olgabot about 4 years ago - 1 comment

#128 - sencha to orpheum

Pull Request - State: closed - Opened by pranathivemuri about 4 years ago - 2 comments

#127 - Add option to remove hashes, e.g. ribosomal seqs

Issue - State: open - Opened by olgabot about 4 years ago - 2 comments
Labels: enhancement

#126 - Separate cell barcode counting and filtering

Issue - State: open - Opened by olgabot about 4 years ago
Labels: enhancement

#125 - Don't save translate CSV or JSON

Pull Request - State: closed - Opened by olgabot about 4 years ago - 1 comment

#124 - Update default translate parameters

Pull Request - State: closed - Opened by olgabot about 4 years ago - 1 comment

#123 - Important! Template update for nf-core/tools v1.12.1

Pull Request - State: closed - Opened by nf-core-bot about 4 years ago - 1 comment

#122 - Output all informational BAM tags to fastq

Pull Request - State: closed - Opened by olgabot about 4 years ago - 1 comment

#121 - template merge

Pull Request - State: closed - Opened by pranathivemuri about 4 years ago

#120 - Important! Template update for nf-core/tools v1.12

Pull Request - State: closed - Opened by nf-core-bot about 4 years ago - 1 comment

#119 - Merging template updates

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 4 comments
Labels: Needs review

#117 - olgabot/sourmash sig merge

Pull Request - State: closed - Opened by olgabot over 4 years ago - 5 comments

#116 - olgabot/do all ksizes at once

Pull Request - State: closed - Opened by olgabot over 4 years ago - 2 comments

#115 - olgabot/sourmash index

Pull Request - State: closed - Opened by olgabot over 4 years ago - 3 comments

#114 - Important! Template update for nf-core/tools v1.11

Pull Request - State: closed - Opened by nf-core-bot over 4 years ago - 2 comments

#113 - address changes in review PR

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 2 comments
Labels: Needs review

#112 - Pseudo PR - community review for initial release

Pull Request - State: closed - Opened by ewels over 4 years ago - 5 comments
Labels: Needs review

#111 - per cell bams

Pull Request - State: closed - Opened by lekhakaranam over 4 years ago - 2 comments

#110 - Template merge

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 1 comment

#109 - add a new release for kmermaid

Issue - State: open - Opened by pranathivemuri over 4 years ago

#108 - merge aligned and unaligned k-mer signatures from single cells

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

#107 - update sencha version

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 3 comments

#106 - no single_ksize, single_molecule, single_log2_sketch_num_hashes for bam

Pull Request - State: closed - Opened by olgabot over 4 years ago - 1 comment

#105 - Increase CPUs, memory, and time for SortMeRNA

Pull Request - State: closed - Opened by olgabot over 4 years ago

#104 - correcting versions and use if not skip_multiqc

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 1 comment
Labels: reviewer can merge

#103 - Use ripgrep to make per-cell fastqs

Pull Request - State: closed - Opened by olgabot over 4 years ago - 1 comment

#102 - Use combine instead of each

Pull Request - State: closed - Opened by olgabot over 4 years ago - 2 comments

#100 - no single_ksize, single_molecule, single_log2_sketch_num_hashes for bam

Pull Request - State: closed - Opened by olgabot over 4 years ago - 1 comment

#99 - tests take too long to run

Issue - State: closed - Opened by phoenixAja over 4 years ago - 1 comment

#98 - removed old sourmash bam2fasta code

Pull Request - State: closed - Opened by phoenixAja over 4 years ago - 1 comment

#97 - Per cell bams

Pull Request - State: closed - Opened by lekhakaranam over 4 years ago

#96 - Add option to make per-cell bam files

Issue - State: open - Opened by olgabot over 4 years ago - 2 comments

#95 - Save sample id to sketch

Pull Request - State: closed - Opened by olgabot over 4 years ago - 1 comment

#94 - updated sencha translate branch

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago

#93 - Template merge

Pull Request - State: closed - Opened by lekhakaranam over 4 years ago - 8 comments

#92 - No TEMPLATE branch

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

#91 - Output to flat directories with sketch ids

Pull Request - State: closed - Opened by olgabot over 4 years ago

#90 - Fix file() issues for S3 outputs

Pull Request - State: closed - Opened by olgabot over 4 years ago - 3 comments

#87 - sourmash compute nucleotide was getting skipped but not peptide - fix the logic for it

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 4 comments
Labels: reviewer can merge

#86 - Add workflow overview image

Pull Request - State: closed - Opened by olgabot over 4 years ago - 8 comments

#85 - adding skip compute

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 3 comments
Labels: reviewer can merge

#84 - lsf yml

Pull Request - State: closed - Opened by lekhakaranam over 4 years ago - 4 comments
Labels: reviewer can merge

#83 - Propagate peptide ksize to sencha translate

Pull Request - State: closed - Opened by olgabot over 4 years ago - 3 comments

#82 - Increase CPUs for high_memory_long

Pull Request - State: closed - Opened by olgabot over 4 years ago

#81 - Add option to use --scaled for sourmash

Pull Request - State: closed - Opened by olgabot over 4 years ago - 4 comments

#80 - Add option to remove ribosomal reads

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#79 - add skip compare

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 3 comments

#73 - Re-add --protein_fastas option

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#71 - change khtools to sencha

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago
Labels: reviewer can merge

#68 - add the correct tags, remove one_signature_per_record, and add the correct size comparison if else loop

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 3 comments
Labels: reviewer can merge

#65 - Update sourmash version

Pull Request - State: closed - Opened by olgabot almost 5 years ago

#64 - correct spelling and trigger docker build

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago

#62 - trigger docker build on dev

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago

#59 - Update process configurations

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#56 - Add docker build github action

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#53 - Replace conflicting things

Pull Request - State: closed - Opened by olgabot almost 5 years ago

#51 - Explicitly state tqdm version

Pull Request - State: closed - Opened by olgabot almost 5 years ago

#50 - Upgrade tqdm to 4.29.1 for tqdm.auto

Issue - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#48 - Add 10x tgz input support with extracting aligned/unaligned reads

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 9 comments

#47 - Add support for aligned/unaligned reads from 10x bam files

Pull Request - State: closed - Opened by olgabot almost 5 years ago

#46 - [WIP] Add fastp support

Pull Request - State: closed - Opened by olgabot almost 5 years ago

#39 - Switch to github actions at some point

Issue - State: closed - Opened by olgabot about 5 years ago - 2 comments
Labels: help wanted, good first issue

#29 - Checklist for 1.0.0 release

Issue - State: closed - Opened by olgabot over 5 years ago - 16 comments

#27 - Only allow PRs to master from dev

Issue - State: closed - Opened by olgabot over 5 years ago - 1 comment

#26 - Actually lint the pipeline code

Issue - State: closed - Opened by olgabot over 5 years ago - 1 comment

#25 - Update to use nf-core/tools with TEMPLATE branch

Issue - State: closed - Opened by olgabot over 5 years ago - 2 comments

#23 - Add ska, seqtk to requirements

Pull Request - State: closed - Opened by olgabot over 5 years ago

#22 - Add python3, bam2fasta, update sourmash in environment.yml

Pull Request - State: closed - Opened by olgabot over 5 years ago

#19 - Split kmer v2

Pull Request - State: closed - Opened by olgabot over 5 years ago - 1 comment

#17 - Extract protein coding sequences before comparing

Pull Request - State: closed - Opened by olgabot over 5 years ago - 1 comment