Code

Add sans-UMI option#128

Code

Merged

ggabernet merged 64 commits intonf-core:devnf-core/airrflow:devfrom dladd:no-umidladd/airrflow:no-umiCopy head branch name to clipboardAug 27, 2021

+810-83

Commits

Commits on Jan 14, 2020

• Merge pull request nf-core#61 from nf-core/dev

  Show description for c3107f3
  ggabernet

  authored
  c3107f3

  Copy full SHA for c3107f3

Commits on Jul 16, 2021

• starting work on no-umi option for bcellmagic

  dladd

  committed
  378998b

  Copy full SHA for 378998b

Commits on Jul 19, 2021

• further work adding a sans-UMI mode, working up through AssemblePairs

  dladd

  committed
  d21924c

  Copy full SHA for d21924c

• merge changes from nf-core/dev

  dladd

  committed
  5a2552f

  Copy full SHA for 5a2552f

• Merge pull request nf-core#113 from nf-core/dev

  Show description for cc29af5
  ggabernet

  authored
  cc29af5

  Copy full SHA for cc29af5

Commits on Jul 20, 2021

• Merge branch 'master' into no-umi

  dladd

  committed
  3c18309

  Copy full SHA for 3c18309

• update schema with no-umi options

  dladd

  committed
  ae048c2

  Copy full SHA for ae048c2

• bugfix: typo on presto_collapseseq parameter specification

  dladd

  committed
  f66509b

  Copy full SHA for f66509b

• add post-assembly versions of presto filterseq and maskprimers for sans-UMI option

  dladd

  committed
  f089285

  Copy full SHA for f089285

Commits on Jul 21, 2021

• add a log parser for no-umi option

  dladd

  committed
  a9e7ca4

  Copy full SHA for a9e7ca4

• bugfix: header parsing for no-umi mode

  dladd

  committed
  a597ea3

  Copy full SHA for a597ea3

• do not require read files to end in _R(1/2)

  dladd

  committed
  83df93c

  Copy full SHA for 83df93c

Commits on Jul 22, 2021

• include light chains (if present) in ParseDB step

  dladd

  committed
  43ded56

  Copy full SHA for 43ded56

Commits on Jul 23, 2021

• allow non-human species in ig shazam tigger threshold

  dladd

  committed
  d169249

  Copy full SHA for d169249

Commits on Jul 27, 2021

• add light chain refs to shazam; allow single-clone samples

  dladd

  committed
  e9dbca1

  Copy full SHA for e9dbca1

Commits on Jul 28, 2021

• Merge branch 'dev' into no-umi

  ggabernet

  authored
  a2f8344

  Copy full SHA for a2f8344

Commits on Jul 29, 2021

• include changeo makedb_args options parameter

  dladd

  committed
  d35c949

  Copy full SHA for d35c949

Commits on Jul 30, 2021

• add fastqc and multiqc section to check stats on assembled and QC-filtered reads (but before collapsing duplicates)

  dladd

  committed
  79d2569

  Copy full SHA for 79d2569

• Merge branch 'dev' into no-umi_dev

  dladd

  committed
  1fc6f85

  Copy full SHA for 1fc6f85

Commits on Aug 2, 2021

• add source label prefix to shazam threshold output files- publishes multiple files to output_dir instead of only one when multiple sources exist

  dladd

  committed
  293c1bf

  Copy full SHA for 293c1bf

• add source label prefixes on output files when loci=tr

  dladd

  committed
  a8c9613

  Copy full SHA for a8c9613

• Hamming dist. thresholding: if # nearest distances < 3, default threshold to 0 and print warning

  dladd

  committed
  de2ea55

  Copy full SHA for de2ea55

Commits on Aug 3, 2021

• add conf file for no-umi test, associated files in nf-core/test-datasets PR nf-core#296

  dladd

  committed
  1381ddf

  Copy full SHA for 1381ddf

• Merge branch 'no-umi' of github.com:dladd/bcellmagic into no-umi

  dladd

  committed
  d4553df

  Copy full SHA for d4553df

Commits on Aug 4, 2021

• remove makedb_args in favor of options.args

  Show description for b630f88
  

  dladd

  and

  ggabernet

  authored
  b630f88

  Copy full SHA for b630f88

• remove makedb_args in favor of options.args

  Show description for 5452213
  

  dladd

  and

  ggabernet

  authored
  5452213

  Copy full SHA for 5452213

• add sourceLabel comment in bin/TIgGER-shazam.R

  Show description for 546e757
  

  dladd

  and

  ggabernet

  authored
  546e757

  Copy full SHA for 546e757

• fix comment in bin/log_parsing_no-umi.py

  Show description for 557f7e7
  

  dladd

  and

  ggabernet

  authored
  557f7e7

  Copy full SHA for 557f7e7

• remove makedb_args in favor of options.args

  Show description for b40a1bf
  

  dladd

  and

  ggabernet

  authored
  b40a1bf

  Copy full SHA for b40a1bf

• remove makedb_args in favor of options.args

  Show description for 908da60
  

  dladd

  and

  ggabernet

  authored
  908da60

  Copy full SHA for 908da60

• use options.args to specify option logic based on config

  Show description for 0ce9e16
  

  dladd

  and

  ggabernet

  authored
  0ce9e16

  Copy full SHA for 0ce9e16

• use options.args to specify option logic based on config

  Show description for 2b214e4
  

  dladd

  and

  ggabernet

  authored
  2b214e4

  Copy full SHA for 2b214e4

• single-ended as reads rather than R1

  Show description for 9dc84fd
  

  dladd

  and

  ggabernet

  authored
  9dc84fd

  Copy full SHA for 9dc84fd

• single-ended as reads rather than R1

  Show description for a82adca
  

  dladd

  and

  ggabernet

  authored
  a82adca

  Copy full SHA for a82adca

• remove commented line

  Show description for e2887d8
  

  dladd

  and

  ggabernet

  authored
  e2887d8

  Copy full SHA for e2887d8

• move postassembly maskprimers and filterseq to their own module files (to be used in sans-umi workflow)

  dladd

  committed
  8ac4850

  Copy full SHA for 8ac4850

Commits on Aug 5, 2021

• resolve conflicts with dev using subworkflow for presto with UMIs

  dladd

  committed
  a3e356e

  Copy full SHA for a3e356e

Commits on Aug 6, 2021

• begin adding sans-umi option as subworkflow: prep work and add fastqc_postassembly

  dladd

  committed
  ea08e17

  Copy full SHA for ea08e17

• add sans-umi subworkflow

  dladd

  committed
  b997c4c

  Copy full SHA for b997c4c

• add no-umi test to CI

  dladd

  committed
  1211d5c

  Copy full SHA for 1211d5c

• simplify/harmonize parameter handling

  dladd

  committed
  e298b60

  Copy full SHA for e298b60

• remove unnecessary param

  dladd

  committed
  c064198

  Copy full SHA for c064198

Commits on Aug 9, 2021

• linting whitespace

  dladd

  committed
  f98b344

  Copy full SHA for f98b344

• testdata URL typo in config

  dladd

  committed
  d619904

  Copy full SHA for d619904

Commits on Aug 11, 2021

• increase collapseseq resource allocation; log parsing: allow underscores in user-defined sample names, remove unused tools in no-umi mode

  dladd

  committed
  0a54c52

  Copy full SHA for 0a54c52

Commits on Aug 12, 2021

• explicitly define default assemblepairs coord as presto

  Show description for 4c589c9
  

  dladd

  and

  ggabernet

  authored
  4c589c9

  Copy full SHA for 4c589c9

• groovy-ify revpr specification in maskprimers

  Show description for 18a550e
  

  dladd

  and

  ggabernet

  authored
  18a550e

  Copy full SHA for 18a550e

• default params.umi_length to null

  Show description for 4034c48
  

  dladd

  and

  ggabernet

  authored
  4034c48

  Copy full SHA for 4034c48

• default params.umi_length to null

  Show description for cadab60
  

  dladd

  and

  ggabernet

  authored
  cadab60

  Copy full SHA for cadab60

• default params.umi_length to null

  Show description for e27f930
  

  dladd

  and

  ggabernet

  authored
  e27f930

  Copy full SHA for e27f930

• add multiqc_config.yaml to files_unchanged for linting

  dladd

  committed
  99a3c84

  Copy full SHA for 99a3c84

• Merge branch 'no-umi' of github.com:dladd/bcellmagic into no-umi

  dladd

  committed
  3879e4c

  Copy full SHA for 3879e4c

• bugfix: explicitly check for undefined umi_length as null

  dladd

  committed
  a6314ab

  Copy full SHA for a6314ab

• linting bugfix: set default umi_length to -1 instead of null

  dladd

  committed
  18a80a0

  Copy full SHA for 18a80a0

Commits on Aug 13, 2021

• Update .nf-core.yml for new linting style

  Show description for f968c9a
  

  dladd

  and

  ggabernet

  authored
  f968c9a

  Copy full SHA for f968c9a

• Update .nf-core.yml

  ggabernet

  authored
  e88431c

  Copy full SHA for e88431c

Commits on Aug 16, 2021

• remove unnecessary sans-UMI parseheader collapse step

  dladd

  committed
  d8dc9d0

  Copy full SHA for d8dc9d0

• revert umi_length to a required param, update docs with no-umi option

  dladd

  committed
  ecc1a9f

  Copy full SHA for ecc1a9f

• remove umi_length requirement from schema again to avoid no-umi automated test bug. The umi_length > 0 check in the pipeline and -1 default should cover this; update changelog

  dladd

  committed
  f7f7bbb

  Copy full SHA for f7f7bbb

• linting whitespace; add recent contributors to README

  dladd

  committed
  9d347cc

  Copy full SHA for 9d347cc

Commits on Aug 17, 2021

• linting whitespace

  dladd

  committed
  b41b8d1

  Copy full SHA for b41b8d1

Commits on Aug 27, 2021

• Update contributors in README.md

  Show description for 4e49c34
  

  dladd

  and

  ggabernet

  authored
  4e49c34

  Copy full SHA for 4e49c34

• asterisks not dashes in README for linting

  dladd

  authored
  b3abe78

  Copy full SHA for b3abe78

• linting

  dladd

  authored
  72893e5

  Copy full SHA for 72893e5