David Arenillas 21dc468dbc7 M Copy commit hash Pull request #5: v0.3.0 Release Merge in RCORBETT/rico from develop to master
* commit '1bf1c0c5f6518ea15d20fd6674de489f2734c44f':
superceded PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv
add new matrix PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv
replace matrix PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv revert rico_processes.nf IPASS back to /... 17 Oct 2024 David Arenillas 1bf1c0c5f65 M Copy commit hash Pull request #4: SDEV-4512 PROFYLE ZERO 767 matrix 20240919 Merge in RCORBETT/rico from SDEV-4512_PROFYLE_ZERO_767_matrix_20240919 to develop
* commit '38f7961550fe6ee969ba5b7f2adb028af61eb91d':
superceded PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv
add new matrix PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv
replace matrix PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv reve... 17 Oct 2024 SDEV-4512 David Arenillas 38f7961550f Copy commit hash superceded PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv 17 Oct 2024 David Arenillas 454ea61e35e Copy commit hash add new matrix PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv 11 Oct 2024 David Arenillas f9505d19363 Copy commit hash replace matrix PROFYLE_ZERO_767_matrix_20240919.tsv with PROFYLE_ZERO_767_matrix_20240919_hgnc.tsv revert rico_processes.nf IPASS back to /rico/IPASS.RData 11 Oct 2024 David Arenillas f8d09ca26f8 Copy commit hash fix IPASS process to use IPASS_hg38.RData 07 Oct 2024 David Arenillas c5e62596474 Copy commit hash change matrix PROFYLE_ZERO_767_matrix_20240919.tsv tab delimiter to space 01 Oct 2024 David Arenillas 8a69ea8bd0b Copy commit hash replace combined_PROFYLE_222_ZERO_matrix.csv with PROFYLE_ZERO_767_matrix_20240919.tsv 26 Sep 2024 David Arenillas 9d7f552ef87 M Copy commit hash Pull request #3: Release v0.2.0 Merge in RCORBETT/rico from develop to master
* commit 'b7814b20db7628258502bf0ef98ef8418dbe6b9b':
remove combined_PROFYLE_222_ZERO_matrix.tsv
bump versione to 0.2.0
replace combined_PROFYLE_222_ZERO_matrix.tsv with combined_PROFYLE_222_ZERO_matrix.csv update rico.repipe files: IPASS_hg38.RData rico/IPASS.RData combined_PROFYLE_222_ZERO_matrix.csv rico/MATRIX.csv
fix minor inde... 16 Sep 2024 David Arenillas b7814b20db7 Copy commit hash remove combined_PROFYLE_222_ZERO_matrix.tsv 09 Sep 2024 David Arenillas aac2a4f5f86 Copy commit hash bump versione to 0.2.0 09 Sep 2024 David Arenillas 052b0350f18 M Copy commit hash Pull request #1: SDEV-4213 - Combined PROFYLE 222 ZERO matrix and replace ipass rdata Merge in RCORBETT/rico from combined_PROFYLE_222_ZERO_matrix_and_replace_ipass_rdata to develop
* commit '8aa758856328121d235e891630c4f6052c11d9da':
replace combined_PROFYLE_222_ZERO_matrix.tsv with combined_PROFYLE_222_ZERO_matrix.csv update rico.repipe files: IPASS_hg38.RData rico/IPASS.RData combined_PROFYLE_222_ZERO_matrix.csv rico/MATRIX.csv
fix minor indentation issues
add ... 06 Sep 2024 SDEV-4213 David Arenillas 8aa75885632 Copy commit hash replace combined_PROFYLE_222_ZERO_matrix.tsv with combined_PROFYLE_222_ZERO_matrix.csv update rico.repipe files:
IPASS_hg38.RData rico/IPASS.RData
combined_PROFYLE_222_ZERO_matrix.csv rico/MATRIX.csv 03 Sep 2024 David Arenillas 7e604d97753 Copy commit hash fix minor indentation issues 30 Aug 2024 David Arenillas ee68a0dcd42 Copy commit hash add params.rico_container in nextflow.config which explicitly specifies the singularity version update rico_processes so they use the params.rico_container from the nextflow.config
remove IPASS.RData now superseded by IPASS_hg38.RData
remove combined_PROFYLE_222_ZERO_matrix.csv preferred by combined_PROFYLE_222_ZERO_matrix.tsv 30 Aug 2024 David Arenillas 2f58da21ec7 Copy commit hash Added install_packages.R Updated rico_processes.nf 21 Aug 2024 David Arenillas 4141ae71c87 Copy commit hash add combined_PROFYLE_222_ZERO_matrix.tsv 30 Jul 2024 David Arenillas 0166ee8da43 Copy commit hash fix IPASS_hg38.RData rico/IPASS.RData 11 Jun 2024 David Arenillas 0f88ef066ef Copy commit hash update to use IPASS_hg38.Rdata 11 Jun 2024 David Arenillas 1e6a4be3fdb M Copy commit hash Merge branch 'hg38_replace_ipass_rdata' into combined_PROFYLE_222_ZERO_matrix_and_replace_ipass_rdata 07 Jun 2024 David Arenillas fa7d3f55a1f Copy commit hash fix rico_processes extract_matrix 06 Jun 2024 David Arenillas 0a6b2142e4d Copy commit hash temporary changes for testing 17 May 2024 David Arenillas 5abfee1fd82 Copy commit hash add combined_PROFYLE_222_Zero_matrix.csv (use csv instead of tsv to be more inline with the original matrix) 03 May 2024 David Arenillas 40ae8c7b518 Copy commit hash replace MATRIX.csv with combined_PROFYLE_222_ZERO_matrix.tsv 30 Apr 2024 David Arenillas c6ab91cd0c0 Copy commit hash replace space with tab separator in M1M2.R MATRIX rico_workflow.nf new file mode 24 Apr 2024 David Arenillas 1d02ca4a54d Copy commit hash deleted copy of original MATRIX.csv 17 Apr 2024 David Arenillas a9d3a58b386 Copy commit hash replace MATRIX.csv with combined_PROFYLE_222_ZERO_matrix.tsv 16 Apr 2024 David Arenillas e37f8e32604 Copy commit hash add IPASS_hg38.RData file replace IPASS.RData file with IPASS_hg38.RData in rico.recipe
- 30 Nov 2023 David Arenillas 5817ff68840 Copy commit hash Revert adding IPASS_hg38.RData on develop instead of feature branch 30 Nov 2023 David Arenillas ea16b1426c2 Copy commit hash add IPASS_hg38.RData file replace IPASS.RData with IPASS_hg38.RData in the rico.recipe 30 Nov 2023 David Arenillas 9afc04a1b7c Copy commit hash update IPASS process to replace IPASS.RData with IPASS_hg38.RData 30 Nov 2023 Richard Corbett e1d4d928d92 M Copy commit hash Merge branch 'master' of https://svn.bcgsc.ca/bitbucket/scm/rcorbett/rico 21 Aug 2023 Richard Corbett 0b80f12fa2d M Copy commit hash Syncing containerdev02 and the filesystem copies. Merge branch 'master' of https://svn.bcgsc.ca/bitbucket/scm/rcorbett/rico 21 Aug 2023 Richard Corbett a107286c46c Copy commit hash Recipe commit from containerdev02 21 Aug 2023 Richard Corbett 7bb01a832e0 Copy commit hash updated README 21 Aug 2023 Richard Corbett 12e20429565 Copy commit hash Fixing for release 0.1.0 21 Jul 2023 Richard Corbett f706dc6d595 Copy commit hash switching to using IPASS from the container 31 May 2023 Richard Corbett ca5a334e339 Copy commit hash Working version using M1M2, IPASS, and new Matrix 31 May 2023 Richard Corbett e8f29df1032 M Copy commit hash Fixing the repo Merge branch 'master' of https://svn.bcgsc.ca/bitbucket/scm/rcorbett/rico 19 May 2023 Richard Corbett 3a98f951db4 Copy commit hash Setting up the IPASS and M1M2 updates 19 May 2023 Richard Corbett 472a8f1e08e Copy commit hash Now processes multiple experimental samples 15 May 2023 Richard Corbett d4b9f3a95d0 Copy commit hash Adding in an M1M2 script. Not working yet 15 May 2023 Richard Corbett 88209abaeb1 Copy commit hash Adding in the IPASS methods. Will report a percentile IPASS score 15 May 2023 Richard Corbett 684abf2a9cf Copy commit hash ADD: Putting in the IPASS scripts and tying up the new version of cibersort 12 May 2023 Richard Corbett 54be35fe103 Copy commit hash Now updates orig LM22 file 13 Mar 2023 Richard Corbett 3daf782895c Copy commit hash Now getting cibersort to run correctly with rico 09 Mar 2023 Richard Corbett c46166ade22 Copy commit hash Removing immunedeconv cibersort 09 Mar 2023 Richard Corbett 7bcb01395ae Copy commit hash Adding standalone cibersort 09 Mar 2023 Richard Corbett ef363cb498c Copy commit hash now using all genes from RSEM output 08 Mar 2023 Richard Corbett c62e5efb833 Copy commit hash README.md edited online with Bitbucket removed image 08 Dec 2022 
David Arenillas
Richard Corbett