LieberInstitute SPEAQeasy issues

LieberInstitute / SPEAQeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

http://lieberinstitute.github.io/SPEAQeasy

MIT License

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issues

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transcript quantification (Salmon/Kallisto) should use trimmed reads

#110 gpertea closed 10 months ago
1
improve storage usage, minimize duplication of FASTQ data

#109 gpertea opened 12 months ago
2
Create a contribution guidelines documentation

#108 lcolladotor opened 12 months ago
0
Adapt code to DSL2

#107 Nick-Eagles closed 10 months ago
0
Add QC metrics generated by Monorail / recount3

#106 lcolladotor opened 12 months ago
0
Add support for MultiQC and maybe other tools

#105 lcolladotor opened 12 months ago
0
Translate course and intro documentation to Spanish

#104 lcolladotor opened 12 months ago
0
Videos documenting how to install and run SPEAQeasy + describing outputs

#103 lcolladotor opened 12 months ago
0
Develop a 1 day (max 2) workshop

#102 lcolladotor opened 12 months ago
0
Guide for all setups that are atypical in some way

#101 lcolladotor opened 12 months ago
0
[JHPCE] repeated fastqc failure on trimmed paired data

#100 gpertea opened 1 year ago
15
BuildAnnotationObjects fails

#99 martinezvbs closed 1 year ago
19
PullTranscriptFasta failing

#98 martinezvbs closed 1 year ago
1
Improve or clarify what's supported for custom annotation

#97 Nick-Eagles opened 1 year ago
0
Add support for more executors

#96 Nick-Eagles opened 1 year ago
0
`BuildAnnotationObjects` halts with current version of R

#95 Nick-Eagles closed 1 year ago
0
Construct `rse_tx` for rat

#94 Nick-Eagles closed 1 year ago
5
InferStrandness failure, --force_strand not supported

#93 gpertea closed 1 year ago
3
allow starting the workflow with existing read alignments (sorted BAM/CRAM files)

#92 gpertea opened 1 year ago
3
Add support for running SPEAQeasy with one sample

#91 Nick-Eagles opened 1 year ago
0
Use fixed version of nextflow

#90 Nick-Eagles closed 2 years ago
0
Store run settings in output objects

#89 Nick-Eagles closed 1 year ago
0
Gene end coordinates don't always agree with GTF

#88 Nick-Eagles closed 1 year ago
2
Provide strandness-inference info in output objects

#87 Nick-Eagles closed 1 year ago
1
Problematic use of caching for docker images

#86 Nick-Eagles closed 2 years ago
0
regtools optimizations

#85 gpertea closed 2 years ago
2
junction start coordinate bug

#84 gpertea closed 2 years ago
1
Failure to build annotation objects for current version of R

#83 Nick-Eagles closed 2 years ago
1
reprocess BrainSeq Phase 1 data

#82 gpertea closed 2 years ago
11
Create Unit Tests

#81 Nick-Eagles opened 2 years ago
0
Some metrics from FastQC are not documented

#80 Nick-Eagles opened 3 years ago
0
R execution breaks on local installations with manually set working directories

#79 Nick-Eagles closed 2 years ago
0
Verify the formatting and contents of `samples.manifest` in `PreprocessInputs`

#78 Nick-Eagles closed 3 years ago
0
Choose whether alignment and/or pseudoalignment are run

#77 Nick-Eagles opened 3 years ago
0
Rename exons with meaningful, unique IDs

#76 Nick-Eagles opened 3 years ago
0
rse_tx: storing counts assay, not just tpm?

#75 gpertea closed 3 years ago
0
"trimmed" and "bamFile" metrics are misleading

#74 Nick-Eagles closed 3 years ago
0
Allocate reasonable memory for counts step on computing clusters

#73 Nick-Eagles opened 3 years ago
1
Problems with package LieberInstitute/jaffelab

#72 ehatl closed 3 years ago
6
Inconsistent compression among samples can break preprocessing step

#71 Nick-Eagles closed 1 year ago
0
trim_mode "adaptive" failure

#70 gpertea closed 3 years ago
0
Update to R 4.0

#69 Nick-Eagles closed 3 years ago
1
Standardize code

#68 lcolladotor closed 3 years ago
0
Make code more robust

#67 lcolladotor closed 3 years ago
2
"How is geneMap$Length generated?" reveals more docs are needed

#66 lcolladotor closed 3 years ago
0
Clean up output from generate_logs.sh

#65 Nick-Eagles opened 3 years ago
1
Add support for passing arbitrary arguments to software

#64 Nick-Eagles closed 3 years ago
0
Input samples are not necessarily mounted with docker

#63 Nick-Eagles closed 4 years ago
0
biomaRt failure

#62 gpertea closed 4 years ago
0
More robust testing across platforms needed with GHA

#61 Nick-Eagles opened 4 years ago
0