CCBR/CHAMPAGNE issues and pull requests

#100 - Create plots with ChIPseeker

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: enhancement

#99 - Consensus peak calling for replicates

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

#98 - Improve GEM CLI calls

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

#97 - Update MACS2 CLI

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

#96 - Fixes to the GEM CLI

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

#95 - macs broad & narrow peaks are same width

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 6 comments
Labels: bug

#94 - Plot distribution of peak widths

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: enhancement

#93 - Overlay/facet Number of Peaks on FRiP plot

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: enhancement

#92 - Calculate and plot Jaccard index on all-vs-all peaks

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

#91 - Group low-resource tasks together in one slurm job?

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: LowPriority

#90 - lint: check that processes specify containers

Issue - State: open - Opened by kelly-sovacool over 1 year ago

#89 - Add processes to calculate and plot Fraction in Peaks

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

#88 - Refactor samplesheet check for flexibility

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 3 comments

#87 - Include peak-specific QC plots in MultiQC report

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

#86 - Optional subworkflow to prepare the genome

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

#85 - Warning message when there are no peaks

Issue - State: open - Opened by kelly-sovacool over 1 year ago

#84 - CLI command to submit slurm batch job

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: cli

#83 - Don't use nextflow module on biowulf or FRCE

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: cli

#82 - Calculate fraction of reads in promoters & enhancer regions

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: enhancement, MediumPriority

#81 - gzip TagAlign files

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

#80 - ci: use build status job for branch protection with matrix

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

#79 - Use 'dir' type and checkIfExists for Channel.fromPath

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

#78 - Error running gem with biowulf slurm executor: genome sequence file not found at directory

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

#77 - Use github actions cache for singularity containers

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

#76 - cache containers between GitHub Actions workflow runs

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: wontfix

#75 - fix(cli): detect host via scontrol

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

#74 - Create working config profile for FRCE

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

#73 - Sometimes singularity uses /home as cache dir

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

#72 - refactor: move qc & peak calling to separate subworkflows

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

#71 - ci: GitHub Actions doesn't run process stubs from alignment onward

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

#70 - refactor to use subworkflows

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#69 - Fix docker containers & bind mounts

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

#68 - 'default' container sometimes overrides other withName/withLabel containers

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

#67 - specify containers in process definitions

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

#66 - Use CCBR logo for multiqc report

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

#65 - config profiles for genomes

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

#64 - Change pip install strategy

Issue - State: closed - Opened by kopardev over 1 year ago - 1 comment
Labels: documentation

#63 - Add PBC ranges to MultiQC text

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

#62 - Fix: multiqc logo

Issue - State: closed - Opened by kopardev over 1 year ago - 1 comment

#61 - Singularity SIF Cachedir

Issue - State: closed - Opened by kopardev over 1 year ago - 4 comments

#60 - Fix: Effective genome size

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

#59 - CLI: command to download singularity/docker cache

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 3 comments
Labels: enhancement, cli

#58 - docker doesn't recognize --bind flag

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

#57 - Use 'process_*' labels to control resources

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#56 - CLI: detect when host is biowulf from VS Code

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: bug, cli

#55 - Use nf-test - unit testing framework with github actions

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment

#54 - CLI: don't fail when env var isn't set

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: bug, cli

#53 - docs: broken bold styling in inserted markdown

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments
Labels: bug, documentation

#52 - Call peaks with macs2, sicer, and gem

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

#51 - Implement main QC steps

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

#50 - bedToBigBed process for IGV

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

#49 - Note encode standards in multqc report

Issue - State: closed - Opened by kelly-sovacool over 1 year ago

#48 - Support datasets without input/igg

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#47 - preseq fails on small test data

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments

#46 - Custom QCstats & QCTable for multiqc report

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: enhancement, HighPriority

#45 - docs: describe sample sheet format

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

#44 - Mark bigWigSum.npz as temporary

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: LowPriority

#43 - sample sheet: add column for replicate

Issue - State: closed - Opened by kelly-sovacool over 1 year ago

#42 - test that check samplesheet throws errors

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment

#41 - Optional process to create sample sheet csv from spreadsheet

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: enhancement, LowPriority

#40 - Create pipeline schema

Issue - State: open - Opened by kelly-sovacool over 1 year ago
Labels: enhancement, LowPriority

#39 - Must use params file to override defaults in nextflow.config

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: documentation

#38 - CLI: modify `-profile` depending on HPC

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: enhancement, LowPriority, cli

#37 - Take sample sheet as input

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#36 - Set nextflow default to NOT kill all processes when one task fails

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#35 - SICER peak caller

Issue - State: closed - Opened by kopardev over 1 year ago - 6 comments
Labels: HighPriority

#34 - GEM peak caller

Issue - State: closed - Opened by kopardev over 1 year ago - 2 comments
Labels: HighPriority

#33 - Set buffer, parallel cores, & tmp file for built-in `sort` command

Issue - State: closed - Opened by kelly-sovacool over 1 year ago

#32 - Annotate peaks w/ UROPA

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: wontfix

#31 - Calculate Jaccard index on all-vs-all peaks

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

#30 - FRiP on called peaks

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments
Labels: HighPriority

#29 - Run MultiQC

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: HighPriority

#28 - Refactor ALIGN_GENOME

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#27 - Export software versions used by all processes

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: enhancement, LowPriority

#26 - Deduplicate reads with macs2

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: HighPriority

#25 - Singularity cache is too large for biowulf home dir

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

#24 - Support paired-end reads

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#23 - CLI: remove conda-related commands

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: cli

#22 - Update citation file after archiving in Zenodo

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: enhancement, LowPriority, cli

#21 - set publishDir mode based on config

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 3 comments
Labels: enhancement, LowPriority

#20 - CLI: only copy default config if nextflow.config doesn't exist

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: bug, cli

#19 - Use nf-core test dataset

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment

#18 - Identify motifs w/ HOMER

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

#17 - Differential peak calling

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: HighPriority

#16 - Call peaks

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments
Labels: HighPriority

#15 - Align to reference genome

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#14 - Align to excluded blacklist regions

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 2 comments
Labels: HighPriority

#13 - QC w/ ngs-qc gen & plot

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 6 comments
Labels: LowPriority

#12 - QC w/ FastqScreen

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#11 - QC w/ FASTQC

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#10 - QC w/ Kraken

Issue - State: open - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: LowPriority

#9 - QC w/ preseq

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments
Labels: HighPriority

#8 - QC w/ PPQT

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#7 - QC w/ Deeptools

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 3 comments
Labels: HighPriority

#6 - Trim raw fastqs

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#5 - Run full SE pipeline QC steps with test data

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#4 - CLI: load HPC modules if host is biowulf

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 4 comments
Labels: cli

#3 - Implement alignment

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

#2 - Implement QC

Issue - State: closed - Opened by kelly-sovacool over 1 year ago
Labels: HighPriority

#1 - Create and/or specify Docker/Singularity containers for each process

Issue - State: closed - Opened by kelly-sovacool over 1 year ago - 1 comment
Labels: HighPriority

GitHub / CCBR/CHAMPAGNE issues and pull requests