Ecosyste.ms: Issues

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

GitHub / rajewsky-lab/spacemake issues and pull requests

#132 - CRAM

Pull Request - State: open - Opened by marvin-jens 10 days ago

#132 - CRAM

Pull Request - State: open - Opened by marvin-jens 10 days ago

#131 - Can't pickle the function mf.parts.bam_writer

Issue - State: open - Opened by falsetry1514 about 1 month ago

#131 - Can't pickle the function mf.parts.bam_writer

Issue - State: open - Opened by falsetry1514 about 1 month ago

#130 - Update docs to kebab notation and other cosmetics

Pull Request - State: open - Opened by nukappa about 1 month ago

#130 - Update docs to kebab notation and other cosmetics

Pull Request - State: open - Opened by nukappa about 1 month ago

#129 - Tool for migrating between versions

Pull Request - State: open - Opened by nukappa about 2 months ago

#129 - Tool for migrating between versions

Pull Request - State: open - Opened by nukappa about 2 months ago

#128 - Wrap minimap2

Pull Request - State: open - Opened by marvin-jens 2 months ago

#127 - Fix newmaster

Pull Request - State: closed - Opened by marvin-jens 3 months ago

#126 - SpacemakeError in get_mapped_BAM_output

Issue - State: closed - Opened by NmnBttr 3 months ago - 8 comments

#125 - Error in detect_tissue: setting an array element with a sequence

Issue - State: open - Opened by QuinceyLv 3 months ago - 2 comments

#124 - error when run 'mamba env create -f environment.yaml'

Issue - State: closed - Opened by lanshui98 5 months ago - 3 comments

#123 - Error in rule run_automatic_analysis

Issue - State: closed - Opened by falsetry1514 7 months ago

#122 - NameError: name 'args' is not defined

Issue - State: closed - Opened by falsetry1514 7 months ago - 2 comments

#121 - CalledprocessError in spacemake run

Issue - State: closed - Opened by falsetry1514 7 months ago - 2 comments

#120 - How to install bcl2fastq2 on Macos

Issue - State: closed - Opened by falsetry1514 7 months ago - 4 comments

#119 - Issues with downsample

Issue - State: open - Opened by nukappa 9 months ago

#118 - downsample wants to downsample everything

Issue - State: open - Opened by nukappa 9 months ago

#117 - Fast cmdline merge

Pull Request - State: closed - Opened by marvin-jens 9 months ago - 1 comment

#114 - Updated docs

Pull Request - State: closed - Opened by nukappa 10 months ago

#113 - Fix star shm concurrency

Pull Request - State: closed - Opened by danilexn 10 months ago - 1 comment

#111 - Updated docs to warn about the GLIBCXX error

Pull Request - State: closed - Opened by nukappa 10 months ago - 1 comment

#110 - try unloading genome before start

Pull Request - State: closed - Opened by danilexn 10 months ago - 3 comments

#109 - critical: fix bug with STAR shared mem

Pull Request - State: closed - Opened by danilexn 10 months ago

#108 - Fix the frame.append warning

Issue - State: open - Opened by nukappa 10 months ago

#107 - Fix the AnnData warning

Issue - State: closed - Opened by nukappa 10 months ago - 2 comments
Labels: deprecation

#106 - WIP: adjacency-aware tile filtering

Pull Request - State: open - Opened by danilexn 10 months ago
Labels: enhancement

#105 - Issues running spacemake on 2B reads

Issue - State: closed - Opened by reubenmoncada 10 months ago

#104 - Updated docs for explaining openst functionality

Pull Request - State: closed - Opened by nukappa 10 months ago

#103 - Bam tag histogram mrfifo

Pull Request - State: closed - Opened by marvin-jens 11 months ago - 7 comments
Labels: enhancement, RAM

#102 - Fastq to ubam port

Pull Request - State: closed - Opened by marvin-jens 11 months ago - 1 comment
Labels: RAM

#101 - Fastq to ubam mrfifo

Pull Request - State: closed - Opened by marvin-jens 12 months ago - 2 comments

#100 - dge: faster & lower RAM usage h5ad creation

Pull Request - State: closed - Opened by danilexn 12 months ago - 3 comments
Labels: RAM

#99 - fastq.py: limit Qres size to keep RAM under control

Pull Request - State: closed - Opened by danilexn 12 months ago - 2 comments
Labels: RAM

#98 - Missing headers in project_df.csv trigger error at startup

Issue - State: closed - Opened by flcvlr 12 months ago - 3 comments
Labels: bug

#97 - 54 ensure map strategy validated

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

#96 - fix #88 name added to configyaml when creating a new run mode

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

#95 - Using checkpoints for a single workflow

Pull Request - State: open - Opened by danilexn about 1 year ago - 4 comments
Labels: enhancement

#94 - Fixes to `fast-cmdline`

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

#93 - Add support for updating R1/R2 in `update_sample`

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

#92 - STAR index with shared memory

Pull Request - State: closed - Opened by danilexn about 1 year ago - 5 comments
Labels: RAM

#91 - Fix merging error

Pull Request - State: closed - Opened by danilexn about 1 year ago - 10 comments
Labels: bug

#90 - Don't add `spatial_barcode_min_matches` on `add_run_mode` with parent mode

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

#89 - Adding run mode with a parent misses one attribute

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

#88 - `name` added to config.yaml when creating a new run mode

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

#87 - fixes error when using `mesh_type=circle`

Pull Request - State: closed - Opened by danilexn about 1 year ago - 1 comment
Labels: bug

#86 - fixes error when using mesh_type `circle`

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

#84 - * change relative import to absolute bc it was causing issues

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

#83 - Ship `openst` barcode_flavor and run_mode with spacemake

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

#80 - samples not correctly read from yaml

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

#79 - Ship `openst` barcode_flavor and run_mode with spacemake

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

#78 - Change join from `inner` to `outer` when stitching pucks

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

#77 - WIP: create reports with python

Pull Request - State: open - Opened by danilexn over 1 year ago - 3 comments
Labels: enhancement

#76 - List of small stuff before freezing paper release

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

#75 - QC_sheet rRNA % is wrong

Issue - State: open - Opened by nukappa over 1 year ago
Labels: bug

#74 - update version number

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

#74 - update version number

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

#73 - Fixes issue #71

Pull Request - State: open - Opened by nukappa over 1 year ago

#73 - Fixes issue #71

Pull Request - State: closed - Opened by nukappa over 1 year ago - 3 comments

#72 - Fix merge issues

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

#71 - Errors when adding barcode_flavor & puck (v0.7.2)

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

#71 - Errors when adding barcode_flavor & puck (v0.7.2)

Issue - State: open - Opened by nukappa over 1 year ago
Labels: bug

#70 - Error when adding the --download_species during init

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

#69 - MissingInputException when merging with 0.7.2

Issue - State: closed - Opened by danilexn over 1 year ago - 2 comments
Labels: bug, documentation

#68 - fix: broken link

Pull Request - State: closed - Opened by J-81 over 1 year ago

#68 - fix: broken link

Pull Request - State: closed - Opened by J-81 over 1 year ago

#67 - WIP: process pucks during downsampling

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

#66 - spatial barcodes are not processed during downsampling

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

#66 - spatial barcodes are not processed during downsampling

Issue - State: open - Opened by danilexn over 1 year ago
Labels: bug

#65 - threads: 1 at automated report and dge creation

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

#65 - threads: 1 at automated report and dge creation

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

#64 - back-porting fast cmdline re-organization from drop-dropseq into master

Pull Request - State: closed - Opened by marvin-jens almost 2 years ago - 9 comments
Labels: enhancement

#63 - error when using mesh_type 'circle'

Issue - State: closed - Opened by LeonDerProfi almost 2 years ago - 1 comment
Labels: bug

#62 - Support for FFPE?

Issue - State: closed - Opened by bernard2012 almost 2 years ago - 2 comments

#61 - automatic stitching and puck filtering

Pull Request - State: closed - Opened by danilexn almost 2 years ago - 6 comments

#60 - Missing input files for rule symlinks

Issue - State: closed - Opened by EugeneEA almost 2 years ago - 4 comments

#59 - List of joined spatial units in meshed adata

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

#58 - List of joined spatial units in meshed adata

Issue - State: closed - Opened by danilexn about 2 years ago - 2 comments

#57 - Potential bug: some log files have 0 size

Issue - State: open - Opened by nukappa about 2 years ago
Labels: drop-dropseq

#56 - loading the STAR mapping index takes long. Treat this as a service

Issue - State: closed - Opened by marvin-jens about 2 years ago
Labels: enhancement

#54 - add/update_sample needs to validate --map_strategy

Issue - State: closed - Opened by marvin-jens about 2 years ago - 3 comments
Labels: enhancement

#53 - Samples merging is broken after updating map_strategy

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

#52 - fixed automated analysis error, closes #51

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

#51 - Automatic analysis still fails sometimes

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

#50 - Replace frame.append with pandas.concat [deprecation warning]

Issue - State: closed - Opened by nukappa about 2 years ago

#49 - Add support for updating R1/R2 in update_sample function

Issue - State: closed - Opened by nukappa about 2 years ago
Labels: enhancement

#48 - Enable parallelism of DGE creation for multiple pucks

Issue - State: closed - Opened by nukappa about 2 years ago
Labels: enhancement

#47 - Fix demux dependency on drop-dropseq branch

Issue - State: closed - Opened by nukappa about 2 years ago
Labels: bug, drop-dropseq

#46 - Replace Bio.pairwise2 with Bio.Align.PairwiseAligner

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

#45 - Update_sample requires species parameter

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

#44 - Change default mapping strategy

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

#43 - Minor fixes and updates

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

#42 - Restrict number of threads for create_spatial_barcode

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

#41 - Possible error that produces empty panels in the qc_sheet

Issue - State: closed - Opened by nukappa about 2 years ago - 4 comments

#40 - Reduce number of threads in fastq -> BAM

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

#39 - restore cmd line functionality for adding barcode_flavor

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