ChristopherBarrington scamp issues

ChristopherBarrington / scamp

single cell analysis and more pipeline

https://christopherbarrington.github.io/scamp/

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Update resources.config

#146 ChristopherBarrington closed 4 weeks ago
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include reporting files

#145 ChristopherBarrington closed 1 month ago
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add mouse+human references

#144 ChristopherBarrington opened 3 months ago
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cell ranger multi count hash not the same

#143 ChristopherBarrington opened 3 months ago
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not all project types listed in guess parameters

#141 ChristopherBarrington opened 3 months ago
1
use project path to guess scamp parameters

#140 ChristopherBarrington opened 3 months ago
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genome information

#139 ChristopherBarrington opened 4 months ago
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137 add genomes to guess parameters

#138 ChristopherBarrington closed 4 months ago
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add drososphila option to guess parameters

#137 ChristopherBarrington closed 4 months ago
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53 add cell ranger multi module and workflow

#136 ChristopherBarrington closed 4 months ago
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reorganise indexes

#135 ChristopherBarrington opened 5 months ago
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determine which cell ranger from project type

#134 ChristopherBarrington opened 5 months ago
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cell ranger multi and arc configs filenames

#133 ChristopherBarrington opened 5 months ago
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restructure cell ranger modules

#132 ChristopherBarrington opened 5 months ago
1
add slurm parameters to config

#131 ChristopherBarrington closed 4 months ago
1
rework guess parameters script

#130 ChristopherBarrington opened 8 months ago
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reorganise task.yaml and publish it

#129 ChristopherBarrington closed 8 months ago
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pipeline fails if fasta file or gtf file are not provided

#128 ChristopherBarrington opened 8 months ago
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provide example params for each workflow

#127 ChristopherBarrington closed 4 months ago
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use task.yaml to store all information

#126 ChristopherBarrington closed 8 months ago
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genome preparation publishes to a directory called null

#125 ChristopherBarrington closed 8 months ago
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Add cat file filter

#124 ChristopherBarrington closed 8 months ago
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update quickstart guide

#123 ChristopherBarrington closed 8 months ago
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rename stages to workflows

#122 ChristopherBarrington closed 8 months ago
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consistent channel dump options

#121 ChristopherBarrington closed 8 months ago
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fix cell ranger mkref editing gtf

#120 ChristopherBarrington closed 8 months ago
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cell ranger mkref edits a potentially linked file

#119 ChristopherBarrington closed 8 months ago
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make genome preparation stages run in parallel

#118 ChristopherBarrington closed 8 months ago
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check template for channel tags

#116 ChristopherBarrington closed 10 months ago
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stages should be workflows

#115 ChristopherBarrington closed 8 months ago
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Add quantified config example

#114 ChristopherBarrington closed 10 months ago
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QC for scATAC analysis with Signac

#113 strohstern opened 11 months ago
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output pipeline reports by default

#112 ChristopherBarrington opened 11 months ago
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update regex in get biomart module

#111 ChristopherBarrington closed 11 months ago
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genome preparation workflow runs in series

#110 ChristopherBarrington closed 8 months ago
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check parameter values

#109 ChristopherBarrington closed 11 months ago
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dump input parameters

#108 ChristopherBarrington closed 8 months ago
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move genome out of dataset parameters

#107 ChristopherBarrington closed 11 months ago
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merge from dev

#105 ChristopherBarrington closed 11 months ago
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use only one genome

#104 ChristopherBarrington closed 11 months ago
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check parameter values

#103 ChristopherBarrington closed 11 months ago
2
unique id is not required

#102 ChristopherBarrington closed 11 months ago
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move genome functions out of subworkflows

#101 ChristopherBarrington closed 11 months ago
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use only one genome

#100 ChristopherBarrington closed 11 months ago
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genome defaults

#99 ChristopherBarrington closed 11 months ago
1
merge yaml with cat module

#98 ChristopherBarrington closed 8 months ago
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unique id is not required

#97 ChristopherBarrington closed 11 months ago
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refactor parameters

#96 ChristopherBarrington closed 11 months ago
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functions in a library

#95 ChristopherBarrington opened 11 months ago
1
refactor parameters

#94 ChristopherBarrington closed 11 months ago
0