Code

Nucleovar Pre-Release Notes #14

Code

Merged

buehlere merged 235 commits intomainmskcc-omics-workflows/nucleovar:mainfrom devmskcc-omics-workflows/nucleovar:devCopy head branch name to clipboardNov 20, 2024

+10,647-1,450

Commits

Commits on Dec 20, 2023

• Redownloaded nf-core vardictjava and wrote code to match inputs without changing original module.

  rnaidu

  committed
  09676dc

  Copy full SHA for 09676dc

Commits on Dec 29, 2023

• Pushing progress on vardictjava.nf

  rnaidu

  committed
  820c639

  Copy full SHA for 820c639

Commits on Jan 5, 2024

• Cleaned up unused code chunks, add fasta, bed, and fai CLI args, and added parameter validation/checking statements in WorkflowNucleovar.groovy

  rnaidu

  committed
  530e62a

  Copy full SHA for 530e62a

• added CLI arguments to nextflow_schema.json to pass linting checks.

  rnaidu

  committed
  68f343c

  Copy full SHA for 68f343c

• adding linting.yml file (unchanged) to pass linting checks.

  rnaidu

  committed
  89251a1

  Copy full SHA for 89251a1

• adding updated nf-core modules to pass linting checks.

  rnaidu

  committed
  b7f3118

  Copy full SHA for b7f3118

• keeping workingd directory up to date to pass lint checks.

  rnaidu

  committed
  67dc6e6

  Copy full SHA for 67dc6e6

• modified inputs to match input cardinality for vardictjava

  rnaidu

  committed
  712ba3d

  Copy full SHA for 712ba3d

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for 0e734f5
  rnaidu

  committed
  0e734f5

  Copy full SHA for 0e734f5

• keeping working branch up to date

  rnaidu

  committed
  03b570d

  Copy full SHA for 03b570d

• added CLI options for vardictjava, module is successfully working in single sample mode.

  rnaidu

  committed
  060f8fb

  Copy full SHA for 060f8fb

Commits on Jan 9, 2024

• Added mutect1 task.ext args in modules.config

  rnaidu

  committed
  2e5185a

  Copy full SHA for 2e5185a

Commits on Jan 11, 2024

• added code to prepare inputs for mutect1 module and added call to mutect1 module (commented out until mutect1 PR has been reviewed)

  rnaidu

  committed
  fa0452b

  Copy full SHA for fa0452b

• created local module for vardict_filtering (utilizing post-processing variant calling docker image) and added to call_variants.nf subworkflows with necessary args

  rnaidu

  committed
  e9def4e

  Copy full SHA for e9def4e

Commits on Jan 17, 2024

• added vardict_filter module and changed acceptance criteria of input BAM files from ArrayList to List type in vardictjava module

  rnaidu

  committed
  0788d06

  Copy full SHA for 0788d06

Commits on Jan 22, 2024

• updated vardict_filter.nf (successfully tested locally on single sample mode)

  rnaidu

  committed
  000cc68

  Copy full SHA for 000cc68

Commits on Jan 25, 2024

• pushing code changes to vardict_filter.nf-- updated module and now successfully working in single and paired sample mode

  rnaidu

  committed
  3d53ba5

  Copy full SHA for 3d53ba5

Commits on Feb 5, 2024

• pushing current work

  rnaidu

  committed
  8d6ea31

  Copy full SHA for 8d6ea31

Commits on Feb 8, 2024

• creating two separate subworkflows for single sample and case control calling and added conditional statement in nucleovar.nf to trigger pipeline depending on number of samples as input. Also clean…

  Show description for a386830
  rnaidu

  committed
  a386830

  Copy full SHA for a386830

Commits on Feb 21, 2024

• pushing work I have so far

  rnaidu

  committed
  1bbd048

  Copy full SHA for 1bbd048

Commits on Apr 10, 2024

• pushing vardictjava

  rnaidu

  committed
  fe26fbe

  Copy full SHA for fe26fbe

Commits on Apr 16, 2024

• cleaning up null directory

  rnaidu

  committed
  d8b7576

  Copy full SHA for d8b7576

• pushing latest commits

  rnaidu

  committed
  967eae9

  Copy full SHA for 967eae9

• removing subworkflows not being used in nucleovar

  rnaidu

  committed
  a569901

  Copy full SHA for a569901

Commits on Apr 24, 2024

• pushing updated work to begin testing on terra

  rnaidu

  committed
  5e60d0e

  Copy full SHA for 5e60d0e

• pushing updated work for cluster testing

  rnaidu

  committed
  2de2d3d

  Copy full SHA for 2de2d3d

Commits on Apr 25, 2024

• Template update for nf-core/tools version 2.13.1

  

  buehlere

  committed
  2f87623

  Copy full SHA for 2f87623

• Merge branch 'TEMPLATE' into feature/call_variants_lsf

  

  buehlere

  committed
  677b945

  Copy full SHA for 677b945

• running on cluster

  

  EricWilliam Buehler

  committed
  c9eb622

  Copy full SHA for c9eb622

Commits on Apr 26, 2024

• pushing work so far with using the updated samplesheet

  rnaidu

  committed
  5b3ab08

  Copy full SHA for 5b3ab08

• commenting out what hasn't been tested yet with the updated samplesheet

  rnaidu

  committed
  092484a

  Copy full SHA for 092484a

• pushing saved work so far before merge

  rnaidu

  committed
  13723bb

  Copy full SHA for 13723bb

• merging feature/call_variants_lsf branch into new_samplesheet

  rnaidu

  committed
  1542231

  Copy full SHA for 1542231

Commits on May 2, 2024

• made necessary code changes listed on clickup to fully transition to new nf-core template and handling of updated samplesheet structure. ready to run on the cluster

  rnaidu

  committed
  b928a01

  Copy full SHA for b928a01

Commits on May 7, 2024

• pushing updated work that runs traceback successfully on a simplex and duplex pair of bams

  rnaidu

  committed
  d3c2fff

  Copy full SHA for d3c2fff

Commits on May 10, 2024

• pushed recent commits, only testing traceback subworkflow

  rnaidu

  committed
  f46b36c

  Copy full SHA for f46b36c

Commits on May 13, 2024

• fasta file passed as channel for proper iteration

  

  EricWilliam Buehler

  committed
  0943261

  Copy full SHA for 0943261

Commits on May 24, 2024

• added curated bams samplesheet into nucleovar and used channel manipulation to prepare inputs for traceback subworkflow

  rnaidu

  committed
  5f46129

  Copy full SHA for 5f46129

Commits on May 28, 2024

• curated bams are being read in through input file and passed directly as inputs to traceback. Also have modified the config files to simplify the nextflow run command for nucleovar and set any defa…

  Show description for cb1ee14
  rnaidu

  committed
  cb1ee14

  Copy full SHA for cb1ee14

Commits on Jun 27, 2024

• updating work on nucleovar

  rnaidu

  committed
  8044973

  Copy full SHA for 8044973

Commits on Jun 28, 2024

• fixing merge conflicts

  rnaidu

  committed
  b7bb63b

  Copy full SHA for b7bb63b

Commits on Jul 1, 2024

• replaced docker image in traceback subworkflow with updated version that removes the id columns, takes in TSV/CSV for file input, and changes data type of start/end coordinate columns to integer.

  rnaidu

  committed
  b94c346

  Copy full SHA for b94c346

Commits on Jul 8, 2024

• pushing updated work on nucleovar -- configuring traceback/pv maf tag to include fillout_type column

  rnaidu

  committed
  8bdeef8

  Copy full SHA for 8bdeef8

• adding basic tumor fillout support, need to fix sync-ing with msk

  

  EricWilliam Buehler

  committed
  1a44f23

  Copy full SHA for 1a44f23

Commits on Jul 9, 2024

• adding filloutype for traceback

  

  EricWilliam Buehler

  committed
  73fd141

  Copy full SHA for 73fd141

Commits on Jul 11, 2024

• Merge pull request #7 from mskcc-omics-workflows/feature/call_variants_type

  Show description for cff0019
  rnaidu

  authored
  cff0019

  Copy full SHA for cff0019

Commits on Jul 24, 2024

• pushing updated work

  rnaidu

  committed
  2cd55dc

  Copy full SHA for 2cd55dc

Commits on Jul 25, 2024

• pushing updated work so faqr

  rnaidu

  committed
  ac29f5d

  Copy full SHA for ac29f5d

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  rnaidu

  committed
  6ff6d4a

  Copy full SHA for 6ff6d4a

• making sure all of traceback is up to date via nf core update command

  rnaidu

  committed
  d965c01

  Copy full SHA for d965c01

Commits on Jul 30, 2024

• pushing updated work on nucleovar

  rnaidu

  committed
  ba69ce4

  Copy full SHA for ba69ce4

• pushing working version of traceback (updated by nf core command)

  rnaidu

  committed
  8291dd7

  Copy full SHA for 8291dd7

Commits on Aug 13, 2024

• pushing updated wok

  rnaidu

  committed
  572fd11

  Copy full SHA for 572fd11

• pushing updated modules

  rnaidu

  committed
  251d648

  Copy full SHA for 251d648

Commits on Aug 15, 2024

• pushing schema json files for the core and aux bams input CSV. renaming samtools and mutect2 modules and uploading nf test config for end to end pipeline nf-test

  rnaidu

  committed
  59ac1f7

  Copy full SHA for 59ac1f7

• changed file extension pattern in schema_input.json

  rnaidu

  committed
  3fda738

  Copy full SHA for 3fda738

Commits on Aug 16, 2024

• pushing updated work

  rnaidu

  committed
  d8b34ab

  Copy full SHA for d8b34ab

• adding bcftools reheader module

  rnaidu

  committed
  3530f06

  Copy full SHA for 3530f06

Commits on Aug 19, 2024

• end to end test

  rnaidu

  committed
  c3135fc

  Copy full SHA for c3135fc

• Merge branch 'dev' into feature/call_variants

  rnaidu

  authored
  e5d6f05

  Copy full SHA for e5d6f05

Commits on Aug 20, 2024

• fixed trailing whitespace

  rnaidu

  committed
  86a41f1

  Copy full SHA for 86a41f1

• passing prettier lint checks

  rnaidu

  committed
  c64c936

  Copy full SHA for c64c936

• passing a test file for lint check

  rnaidu

  committed
  916f036

  Copy full SHA for 916f036

• passing lint check

  rnaidu

  committed
  d88f1e5

  Copy full SHA for d88f1e5

• trying to invoke nf-core lint check

  rnaidu

  committed
  1d790b8

  Copy full SHA for 1d790b8

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for 3dcfcf7
  rnaidu

  committed
  3dcfcf7

  Copy full SHA for 3dcfcf7

• testing a portion of nucleovar to kick off github actions

  rnaidu

  committed
  0cc9229

  Copy full SHA for 0cc9229

• pass linting check

  rnaidu

  committed
  b84d64a

  Copy full SHA for b84d64a

• trying to pass nf-core lint check

  rnaidu

  committed
  b603b6c

  Copy full SHA for b603b6c

• passed nf stub test

  rnaidu

  committed
  b09300a

  Copy full SHA for b09300a

• passing test

  rnaidu

  committed
  5d08cde

  Copy full SHA for 5d08cde

• fixing file permissions to test runs

  rnaidu

  committed
  2ba96b8

  Copy full SHA for 2ba96b8

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for a7e02ac
  rnaidu

  committed
  a7e02ac

  Copy full SHA for a7e02ac

• trying to pass test profile

  rnaidu

  committed
  8aa113b

  Copy full SHA for 8aa113b

• reorganizing modules so that local modules and nf-core modules are not mixed up

  rnaidu

  committed
  2c365d2

  Copy full SHA for 2c365d2

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for d3e31c6
  rnaidu

  committed
  d3e31c6

  Copy full SHA for d3e31c6

• removing tabix and bgzip nf core modules as they are not used

  rnaidu

  committed
  6f90f85

  Copy full SHA for 6f90f85

• passing prettier lint check

  rnaidu

  committed
  add647e

  Copy full SHA for add647e

• added stub test with dummy data

  rnaidu

  committed
  2c1dd39

  Copy full SHA for 2c1dd39

• adding stub profile

  rnaidu

  committed
  cde8262

  Copy full SHA for cde8262

• getting stub test to run

  rnaidu

  committed
  fa37f62

  Copy full SHA for fa37f62

• adding relative path for inputs

  rnaidu

  committed
  415426a

  Copy full SHA for 415426a

• add dummy relative path data for all inputs

  rnaidu

  committed
  dfd2ae2

  Copy full SHA for dfd2ae2

• dummy data upload

  rnaidu

  committed
  0c75d96

  Copy full SHA for 0c75d96

• upload dummy samplesheet

  rnaidu

  committed
  362a825

  Copy full SHA for 362a825

• final links to dummy data

  rnaidu

  committed
  8611aa7

  Copy full SHA for 8611aa7

• uploading saplesheet

  rnaidu

  committed
  6e99e68

  Copy full SHA for 6e99e68

• updated configs

  rnaidu

  committed
  1efebc1

  Copy full SHA for 1efebc1

• removing schema json

  rnaidu

  committed
  0b24695

  Copy full SHA for 0b24695

Commits on Aug 22, 2024

• replacing ci.yml command with nf-test

  rnaidu

  committed
  611e691

  Copy full SHA for 611e691

Commits on Aug 23, 2024

• updating ci.yml with direct path to nucleovar.nf instead for stub test

  rnaidu

  committed
  a04a2d6

  Copy full SHA for a04a2d6

• changing relative path in ci.yml

  rnaidu

  committed
  8ab4aa5

  Copy full SHA for 8ab4aa5

• test

  rnaidu

  committed
  150a5d7

  Copy full SHA for 150a5d7

• test

  rnaidu

  committed
  96d9eaa

  Copy full SHA for 96d9eaa

• adding in nf-test command

  rnaidu

  committed
  6107d85

  Copy full SHA for 6107d85

• testing nf-test command

  rnaidu

  committed
  ea81b6f

  Copy full SHA for ea81b6f

• updating nf-test paths

  rnaidu

  committed
  281d530

  Copy full SHA for 281d530

• isolating stub test only

  rnaidu

  committed
  bc16f06

  Copy full SHA for bc16f06

Commits on Aug 26, 2024

• replacing all filepaths in aux bams csv to null

  rnaidu

  committed
  c586c7c

  Copy full SHA for c586c7c

Commits on Sep 2, 2024

• removed projectDir from paths in stub pipeline input CSV file and removed v1.0 data folder to keep data secure

  rnaidu

  committed
  4e839e3

  Copy full SHA for 4e839e3

• changed filepaths on stub csv file

  rnaidu

  committed
  c9880ae

  Copy full SHA for c9880ae

• working nf test

  rnaidu

  committed
  195e36a

  Copy full SHA for 195e36a

• working stub test in nextflow run command to

  rnaidu

  committed
  62a7e01

  Copy full SHA for 62a7e01

• updated ci.yml

  rnaidu

  committed
  8a98388

  Copy full SHA for 8a98388

• seeing if singularity profile works

  rnaidu

  committed
  10c2352

  Copy full SHA for 10c2352

• updating ci.yml

  rnaidu

  committed
  9477ea5

  Copy full SHA for 9477ea5

• testing up until mutect2

  rnaidu

  committed
  6677809

  Copy full SHA for 6677809

• stub test working all the way until mutect2

  rnaidu

  committed
  0b4dfef

  Copy full SHA for 0b4dfef

• updated stub config

  rnaidu

  committed
  93eb569

  Copy full SHA for 93eb569

Commits on Sep 3, 2024

• stub test working up until vardict filter

  rnaidu

  committed
  88104db

  Copy full SHA for 88104db

• stub test working until mutect2 and changed up paths in casecontrol call variants subworkflow

  rnaidu

  committed
  dd07246

  Copy full SHA for dd07246

• stub test working up until bcftools mutect

  rnaidu

  committed
  62b1494

  Copy full SHA for 62b1494

• both regular and stub test working up until end of genome nexus

  rnaidu

  committed
  31812d7

  Copy full SHA for 31812d7

Commits on Sep 4, 2024

• adding in the header and sample order files

  rnaidu

  committed
  fc8cf99

  Copy full SHA for fc8cf99

• regular and stub test working up until end of traceback

  rnaidu

  committed
  80ba3ba

  Copy full SHA for 80ba3ba

• stub test working end to end pipeline

  rnaidu

  committed
  b9e002a

  Copy full SHA for b9e002a

• stub test working end to end and fixing lint check

  rnaidu

  committed
  847f26f

  Copy full SHA for 847f26f

• removing fasta files from stub folder since nf-core data paths are given in config file

  rnaidu

  committed
  347601a

  Copy full SHA for 347601a

• ran prettier on modules.json

  rnaidu

  committed
  67591b2

  Copy full SHA for 67591b2

• trying to pass nf-core lint check with automatic fixes

  rnaidu

  committed
  9fe8874

  Copy full SHA for 9fe8874

Commits on Sep 5, 2024

• updated linting.yml to properly show which modules are failing

  rnaidu

  committed
  933c538

  Copy full SHA for 933c538

• changing python version

  rnaidu

  committed
  f867b82

  Copy full SHA for f867b82

• change python version in linting.yml back to 3.12

  rnaidu

  committed
  a9a08ad

  Copy full SHA for a9a08ad

• reformatting modules.json to pass prettier lint check

  rnaidu

  committed
  d6cfd51

  Copy full SHA for d6cfd51

Commits on Sep 6, 2024

• added stub annotated maf for vcf2maf genome nexus module

  rnaidu

  committed
  edda31e

  Copy full SHA for edda31e

• changed stub file extension

  rnaidu

  committed
  be9d690

  Copy full SHA for be9d690

Commits on Sep 9, 2024

• Create input.template.json

  

  buehlere

  committed
  a4a0930

  Copy full SHA for a4a0930

Commits on Sep 10, 2024

• updated genome nexus subworkflow to pass lint check, added https prefix in schemas to pass nf-core lint

  rnaidu

  committed
  4545c91

  Copy full SHA for 4545c91

• changed branch of install in modules.json

  rnaidu

  committed
  51cb1eb

  Copy full SHA for 51cb1eb

• formatted file

  rnaidu

  committed
  3d81a23

  Copy full SHA for 3d81a23

• updated mutect1 module with local changes to pass nf-core lint check

  rnaidu

  committed
  a1e1845

  Copy full SHA for a1e1845

• fixed other lint fails aside from traceback subworkflow update

  rnaidu

  committed
  28b694a

  Copy full SHA for 28b694a

• passing prettier lint

  rnaidu

  committed
  d29d986

  Copy full SHA for d29d986

• removing files accidentally committed

  rnaidu

  committed
  7c9221e

  Copy full SHA for 7c9221e

• adding newline in sample vcf to pass prettier

  rnaidu

  committed
  8f043ae

  Copy full SHA for 8f043ae

• passing more prettier checks

  rnaidu

  committed
  c0be774

  Copy full SHA for c0be774

Commits on Sep 11, 2024

• adding additional input parameters

  

  buehlere

  committed
  38cd349

  Copy full SHA for 38cd349

• publishing stub files so all input parameters are up to date

  rnaidu

  committed
  c031f2e

  Copy full SHA for c031f2e

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for c37f480
  rnaidu

  committed
  c37f480

  Copy full SHA for c37f480

• added stub canonical target tx ref file

  rnaidu

  committed
  0a90356

  Copy full SHA for 0a90356

• completing all github action checks and addition of canonical tx ref file parameter

  rnaidu

  committed
  3738f2e

  Copy full SHA for 3738f2e

• passing prettier checks

  rnaidu

  committed
  c2e405e

  Copy full SHA for c2e405e

• modules.json prettier lint fix

  rnaidu

  committed
  a9d7a74

  Copy full SHA for a9d7a74

Commits on Sep 12, 2024

• Update input.template.json

  

  buehlere

  committed
  35083ce

  Copy full SHA for 35083ce

• moved sample_order_file creation to before nucleovar.nf and made it so the file is being created within the script itself.

  rnaidu

  committed
  91caa99

  Copy full SHA for 91caa99

• Merge branch 'feature/call_variants' of https://github.com/mskcc-omics-workflows/nucleovar into feature/call_variants

  Show description for 8331b72
  rnaidu

  committed
  8331b72

  Copy full SHA for 8331b72

• adding test push

  rnaidu

  committed
  f18d62a

  Copy full SHA for f18d62a

• removal of test.txt file

  rnaidu

  committed
  64241ae

  Copy full SHA for 64241ae

• Merge pull request #1 from mskcc-omics-workflows/feature/call_variants

  Show description for 88b5193
  rnaidu

  authored
  88b5193

  Copy full SHA for 88b5193

• Update input.template.json

  

  buehlere

  committed
  5c37c7d

  Copy full SHA for 5c37c7d

Commits on Sep 13, 2024

• incorrect name

  

  buehlere

  committed
  ec07372

  Copy full SHA for ec07372

Commits on Sep 16, 2024

• Update nextflow.config

  buehlere

  authored
  00274f2

  Copy full SHA for 00274f2

• Update inputs.template.json

  

  buehlere

  committed
  f6472db

  Copy full SHA for f6472db

• Update inputs.template.json

  

  buehlere

  committed
  f6b84c5

  Copy full SHA for f6b84c5

• Update inputs.template.json

  

  buehlere

  committed
  2c7e9a2

  Copy full SHA for 2c7e9a2

• Update nextflow_schema.json

  

  buehlere

  committed
  80d4790

  Copy full SHA for 80d4790

Commits on Sep 17, 2024

• updating conf

  

  buehlere

  committed
  55d7ed8

  Copy full SHA for 55d7ed8

• Update inputs.template.json

  

  buehlere

  committed
  2b84b16

  Copy full SHA for 2b84b16

• Update nextflow_schema.json

  

  buehlere

  committed
  33cb01f

  Copy full SHA for 33cb01f

• Update nucleovar.nf

  

  buehlere

  committed
  83968d3

  Copy full SHA for 83968d3

• Update nucleovar.nf

  

  buehlere

  committed
  ed2700e

  Copy full SHA for ed2700e

• Update nucleovar.nf

  

  buehlere

  committed
  5cb6362

  Copy full SHA for 5cb6362

• Update inputs.template.json

  

  buehlere

  committed
  c334d87

  Copy full SHA for c334d87

• Update main.nf

  

  buehlere

  committed
  4fc11a4

  Copy full SHA for 4fc11a4

Commits on Sep 18, 2024

• Update nextflow.config

  buehlere

  authored
  4757fef

  Copy full SHA for 4757fef

Commits on Sep 25, 2024

• pushing test file to start PR

  rnaidu

  committed
  49dbb92

  Copy full SHA for 49dbb92

• pulling dev branch so everything is up to date

  rnaidu

  committed
  e87ed72

  Copy full SHA for e87ed72

Commits on Sep 26, 2024

• changed pre-nucleovar.nf code so that input samplesheets take in only the bam paths and find the bai paths using nextflow logic instead of a hard-coded .bai filepath

  rnaidu

  committed
  9ac6299

  Copy full SHA for 9ac6299

• added hotspots as a mandatory CLI parameter and updated nucleovar.nf and config files accordingly. also modified maf_processing module to include the hotspots file and use the correct docker image …

  Show description for 2cd1f24
  rnaidu

  committed
  2cd1f24

  Copy full SHA for 2cd1f24

• testing voyager inputs

  

  EricWilliam Buehler

  committed
  7e545fe

  Copy full SHA for 7e545fe

• putting new stub files on github repo for stub config

  rnaidu

  committed
  fc8e34c

  Copy full SHA for fc8e34c

• updated stub files for stub config

  rnaidu

  committed
  067becc

  Copy full SHA for 067becc

• maf processing update

  

  EricWilliam Buehler

  committed
  ff2f43e

  Copy full SHA for ff2f43e

• keeping all edits made in dev up to date to prepare for PR

  rnaidu

  committed
  abacbd0

  Copy full SHA for abacbd0

• moved work I did on dev branch to nucleovar_v2_fixes. this is running end to end

  rnaidu

  committed
  f062fa5

  Copy full SHA for f062fa5

Commits on Sep 27, 2024

• changed line of code in utils_nfcore_nucleovar_pipeline to extract correct duplex and simplex bai files

  rnaidu

  committed
  b6aaad9

  Copy full SHA for b6aaad9

• replaced all postprocessing docker image with the latest release and commented out code cleanup in bcftools_vardict.nf. also made sure maf_processing module is using correct command name

  rnaidu

  committed
  571a07d

  Copy full SHA for 571a07d

Commits on Sep 30, 2024

• working end to end stub test

  rnaidu

  committed
  c07aa27

  Copy full SHA for c07aa27

Commits on Oct 1, 2024

• passing lint and prettier checks

  rnaidu

  committed
  f0450f1

  Copy full SHA for f0450f1

• test push

  rnaidu

  committed
  1a13573

  Copy full SHA for 1a13573

• lint checks cont

  rnaidu

  committed
  bfcb910

  Copy full SHA for bfcb910

• passing remaining checks

  rnaidu

  committed
  befc4aa

  Copy full SHA for befc4aa

• added the meta.yml for genotypevariants in prettierignore file until markdown schema consensus is made

  rnaidu

  committed
  d2b4037

  Copy full SHA for d2b4037

• running stub test

  rnaidu

  committed
  0c97022

  Copy full SHA for 0c97022

Commits on Oct 2, 2024

• Merge pull request #11 from mskcc-omics-workflows/nucleovar_v2_fixes

  Show description for 742f5b5
  buehlere

  authored
  742f5b5

  Copy full SHA for 742f5b5

• Update nextflow_schema.json

  

  buehlere

  committed
  1fc9c83

  Copy full SHA for 1fc9c83

• Update nucleovar.nf

  

  buehlere

  committed
  7c2e964

  Copy full SHA for 7c2e964

Commits on Oct 4, 2024

• edits for running on lsf

  

  EricWilliam Buehler

  committed
  6293262

  Copy full SHA for 6293262

• Merge branch 'dev' into lsf-fix

  

  buehlere

  committed
  0afdbaf

  Copy full SHA for 0afdbaf

• config update

  

  EricWilliam Buehler

  committed
  612cf60

  Copy full SHA for 612cf60

• Merge pull request #16 from mskcc-omics-workflows/lsf-fix

  Show description for 93557d0
  buehlere

  authored
  93557d0

  Copy full SHA for 93557d0

• config update

  

  EricWilliam Buehler

  committed
  fb9d9d9

  Copy full SHA for fb9d9d9

Commits on Oct 8, 2024

• test push to start enhancements v2 PR

  rnaidu

  committed
  d42cee1

  Copy full SHA for d42cee1

Commits on Oct 9, 2024

• organized each variant caller in its own subworkflow,removed any subworkflows/modules not being used, added vardict_header_file as CLI input and changed configs accordingly, added correct version o…

  Show description for bbddc84
  rnaidu

  committed
  bbddc84

  Copy full SHA for bbddc84

• removed norm/sorting for complexvar VarDict VCFs

  rnaidu

  committed
  05677d3

  Copy full SHA for 05677d3

• condensed target_bed_file prep into a subworkflow to clean up nucleovar.nf and added outputs of nucleovar to be emitted. Also added a publishDir statement in last moddule but commented out for now

  rnaidu

  committed
  34acd77

  Copy full SHA for 34acd77

• passing prettier lint checks

  rnaidu

  committed
  9a91d2c

  Copy full SHA for 9a91d2c

• accidentally pushed sample_order file, its not needed

  rnaidu

  committed
  e3719c1

  Copy full SHA for e3719c1

• fixed indentation for juno.config to pass prettier check

  rnaidu

  committed
  9537667

  Copy full SHA for 9537667

• trying to pass prettier check

  rnaidu

  committed
  1ea9e55

  Copy full SHA for 1ea9e55

Commits on Oct 10, 2024

• Update nucleovar.nf

  

  buehlere

  committed
  7be915c

  Copy full SHA for 7be915c

• changing tab spacing for config file to pass linting

  rnaidu

  committed
  953e927

  Copy full SHA for 953e927

• Merge branch 'dev' into feature/enhancements_v2

  rnaidu

  authored
  9fedf3a

  Copy full SHA for 9fedf3a

• removed header files as mandatory CLI input and instead used global variable to set their path as a channel in nucleovar

  rnaidu

  committed
  190fa3d

  Copy full SHA for 190fa3d

• Merge branch 'feature/enhancements_v2' of https://github.com/mskcc-omics-workflows/nucleovar into feature/enhancements_v2

  Show description for c43290d
  rnaidu

  committed
  c43290d

  Copy full SHA for c43290d

• removing txt file not needed

  rnaidu

  committed
  7c12ca9

  Copy full SHA for 7c12ca9

• emit samplesheets as output in case they are needed downstream

  rnaidu

  committed
  0955bdd

  Copy full SHA for 0955bdd

• remove text file

  rnaidu

  committed
  707f370

  Copy full SHA for 707f370

• fixed linting

  rnaidu

  committed
  861d68c

  Copy full SHA for 861d68c

• Update nucleovar.nf

  

  buehlere

  committed
  9b218b0

  Copy full SHA for 9b218b0

• added README for stub and v1.0 asset files

  rnaidu

  committed
  cf0c972

  Copy full SHA for cf0c972

• Merge branch 'dev' into feature/enhancements_v2

  rnaidu

  authored
  673e374

  Copy full SHA for 673e374

• commenting out

  rnaidu

  committed
  7366cf2

  Copy full SHA for 7366cf2

• Merge branch 'feature/enhancements_v2' of https://github.com/mskcc-omics-workflows/nucleovar into feature/enhancements_v2

  Show description for 1dcdc46
  rnaidu

  committed
  1dcdc46

  Copy full SHA for 1dcdc46

• pushing updates

  rnaidu

  committed
  601e37f

  Copy full SHA for 601e37f

Commits on Oct 11, 2024

• removed creation of sample order text file in nextflow and put within scope of bcftools reheader module to avoid sample switchup when running on diff nodes. also updated test config with correct fi…

  Show description for 00a5a0a
  rnaidu

  committed
  00a5a0a

  Copy full SHA for 00a5a0a

Commits on Oct 16, 2024

• Update nucleovar.nf

  

  buehlere

  committed
  2a5d6aa

  Copy full SHA for 2a5d6aa

Commits on Oct 17, 2024

• adding nfprov for output info

  

  EricWilliam Buehler

  committed
  f75a929

  Copy full SHA for f75a929

Commits on Oct 18, 2024

• specifying directory for manifest

  

  EricWilliam Buehler

  committed
  31c7447

  Copy full SHA for 31c7447

• Revert "specifying directory for manifest"

  Show description for b99e0be
  

  buehlere

  committed
  b99e0be

  Copy full SHA for b99e0be

• update config

  

  EricWilliam Buehler

  committed
  91d18e2

  Copy full SHA for 91d18e2

• update config

  

  EricWilliam Buehler

  committed
  d6cbc8a

  Copy full SHA for d6cbc8a

• adding nf-prov

  

  EricWilliam Buehler

  committed
  113d15e

  Copy full SHA for 113d15e

Commits on Oct 21, 2024

• nfprov config

  

  EricWilliam Buehler

  committed
  8119f1b

  Copy full SHA for 8119f1b

Commits on Nov 13, 2024

• Update nextflow.config

  

  buehlere

  committed
  638631b

  Copy full SHA for 638631b

• linting

  

  buehlere

  committed
  7a59157

  Copy full SHA for 7a59157

• Update ci.yml

  

  buehlere

  committed
  954cffc

  Copy full SHA for 954cffc

• lint

  

  buehlere

  committed
  b624691

  Copy full SHA for b624691

• Update nextflow.config

  

  buehlere

  committed
  64c65b2

  Copy full SHA for 64c65b2

Commits on Nov 20, 2024

• syncing the README and associated files with the voyager tested nucleovar branch

  rnaidu

  committed
  f438ae0

  Copy full SHA for f438ae0

• Merge branch 'dev' into feature/enhancements_v2

  buehlere

  authored
  7e39826

  Copy full SHA for 7e39826

• Update nextflow.config

  

  buehlere

  committed
  8912635

  Copy full SHA for 8912635

• Update nextflow.config

  

  buehlere

  committed
  135fe22

  Copy full SHA for 135fe22

• Update nextflow.config

  

  buehlere

  committed
  599e761

  Copy full SHA for 599e761

• Merge pull request #17 from mskcc-omics-workflows/feature/enhancements_v2

  Show description for 29df9db
  buehlere

  authored
  29df9db

  Copy full SHA for 29df9db