NYU-Molecular-Pathology NGS580-nf issues

NYU-Molecular-Pathology / NGS580-nf

Target exome sequencing analysis for NYU NGS580 gene panel

GNU General Public License v3.0

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issues

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R installed in home dir breaks Singularity containers

#43 varshini712 opened 4 years ago
2
Remove 'done' channels

#42 stevekm opened 5 years ago
0
Need to refactor channel `create` method

#41 stevekm opened 5 years ago
0
Updated samplesheets do not seem to always work correctly with 'resume'

#40 stevekm opened 5 years ago
0
Sometimes values loaded from JSON are not available inside processes

#39 stevekm opened 5 years ago
0
Evaluate Nextflow Tower integration

#38 stevekm opened 5 years ago
0
Need to adjust memory allocation for jobs

#37 stevekm opened 5 years ago
0
Use full git tag in output tables

#36 stevekm closed 5 years ago
1
Need output validator

#35 stevekm opened 5 years ago
0
masked nucleotides showing up in vcf files, breaking merge script

#34 stevekm closed 5 years ago
0
Need to include `finalize-work-rm` in with default `run` Makefile recipe

#33 stevekm closed 5 years ago
0
Refactor variant calling processes to use separate normalize_vcf steps

#32 stevekm opened 5 years ago
0
LoFreq Somatic output include dbSNP variants

#31 stevekm closed 5 years ago
0
rename karyotype plots

#30 stevekm opened 5 years ago
0
Need scope writeup

#29 stevekm opened 5 years ago
0
re-setup vaf distribution plot

#28 stevekm opened 5 years ago
0
Need to update coverage cutoffs

#27 stevekm opened 5 years ago
0
sometimes custom analysis report does not run

#26 stevekm opened 5 years ago
2
need bash trap for .nextflow.submitted

#25 stevekm closed 5 years ago
2
Errors in `reformat-vcf-table.py` return exit code 0

#24 stevekm opened 5 years ago
2
Need to refactor pairs channels to include 'callerType'

#23 stevekm closed 5 years ago
0
Need writeup for CNV Pool reference file generation workflow

#22 stevekm opened 5 years ago
0
remove process lofreq_filter_reformat from config

#21 stevekm opened 5 years ago
0
Need karyotype plot

#20 stevekm closed 5 years ago
0
Need to refactor LoFreq and HaplotypeCaller to use separate filter and tsv processes

#19 stevekm closed 5 years ago
0
Need to update TMB calculation methods for pairs, unpaired samples

#18 stevekm closed 5 years ago
0
Need to run genomic signatures for all variant callers

#17 stevekm closed 5 years ago
0
Add CNVKit targets annotation file creation method

#16 stevekm closed 5 years ago
1
Add configs for different targets.bed files

#15 stevekm closed 5 years ago
0
Add subdirs to publishDirs for .bam files

#14 stevekm closed 5 years ago
1
Need to refactor variable name in cnvkit process

#13 stevekm closed 5 years ago
0
resume not working with RealignerTargetCreator step

#12 stevekm closed 5 years ago
1
Fix failed tumor-normal comparison log in report

#11 stevekm closed 5 years ago
1
need to refactor reference file staging methods

#10 stevekm closed 5 years ago
2
need to update ref download methods

#9 stevekm closed 5 years ago
1
docker build error

#8 hmkim closed 5 years ago
6
filter for fastq with no reads

#7 stevekm closed 5 years ago
3
add FACETS to pipeline

#6 stevekm closed 5 years ago
0
split bam_ra_rc_gatk process

#5 stevekm closed 5 years ago
0
Need to support deployment with multiple fastq directories

#4 stevekm closed 6 years ago
1
Update QC report metrics

#3 stevekm closed 5 years ago
1
Make 'no lane split' default for samplesheet via deployment setup

#2 stevekm closed 6 years ago
1
copy samplesheet to output dir

#1 stevekm closed 5 years ago
0