From bdcf9e25dca22965acc112ed7d8ae9b360af2583 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 09:24:02 -0400 Subject: [PATCH 1/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index dfda2e5cb..ee49a5238 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -1,4 +1,20 @@ +# (next version) +2020-04-24 (Date of Last Commit) + +* Added new snRNAseq counting_mode parameter + * For the sn_rna couting mode only, updated dropseq tools to version # + * Updated sctools to version # to support new counting + +* Added tests for sn_rna counting mode + +* Updated Zarr and Loom output to include global attribute for counting mode + +* Updated documentation to detail new counting_mode parameter and to include new FAQ section + + + # optimus_v2.0.0 +2020-02-28 (Date of Last Commit) * Fixed bug that resulted in emptyDrops output being incorrect From f6698c648a2a8207b0fb3fe5d281f18fc13bdc28 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 10:07:07 -0400 Subject: [PATCH 2/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index ee49a5238..5d344f45d 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -1,15 +1,17 @@ # (next version) 2020-04-24 (Date of Last Commit) -* Added new snRNAseq counting_mode parameter - * For the sn_rna couting mode only, updated dropseq tools to version # - * Updated sctools to version # to support new counting +* Added a new counting_mode parameter to run the workflow for single-nuclei datasets + * Updated Drop-seq tools to v2.3.0; this update is the single-nuclei parameter (counting_mode = sn_rna) + * Updated sctools to support the single-nuclei parameter (counting_mode = sn_rna) -* Added tests for sn_rna counting mode +* Added tests for running the workflow when counting_mode = sn_rna -* Updated Zarr and Loom output to include global attribute for counting mode +* Updated the Zarr and Loom output to include a global attribute describing the counting mode -* Updated documentation to detail new counting_mode parameter and to include new FAQ section +* Added new example datasets that can be used with the Optimus workflow + +* Updated the README documentation to detail the new counting_mode parameter, describe example datasets, and to include a new FAQ section From a0ea6e671acdc272fabddd6bea023619fb653dc4 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 10:08:31 -0400 Subject: [PATCH 3/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index 5d344f45d..57f1f9bf1 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -2,7 +2,7 @@ 2020-04-24 (Date of Last Commit) * Added a new counting_mode parameter to run the workflow for single-nuclei datasets - * Updated Drop-seq tools to v2.3.0; this update is the single-nuclei parameter (counting_mode = sn_rna) + * Updated Drop-seq tools to v2.3.0; this update is only used when the workflow is set to the single-nuclei mode (counting_mode = sn_rna) * Updated sctools to support the single-nuclei parameter (counting_mode = sn_rna) * Added tests for running the workflow when counting_mode = sn_rna From 2ea099adc03f2ac966be25ac0b916d1e520013bc Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 10:10:38 -0400 Subject: [PATCH 4/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index 57f1f9bf1..d44a4c6b5 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -1,9 +1,11 @@ # (next version) 2020-04-24 (Date of Last Commit) -* Added a new counting_mode parameter to run the workflow for single-nuclei datasets - * Updated Drop-seq tools to v2.3.0; this update is only used when the workflow is set to the single-nuclei mode (counting_mode = sn_rna) - * Updated sctools to support the single-nuclei parameter (counting_mode = sn_rna) +* Added a new counting_mode parameter to Optimus workflow which enables processing of single-nuclei datasets + +* Updated Drop-seq tools to v2.3.0; this update is only used when the workflow is set to the single-nuclei mode (counting_mode = sn_rna) + +* Updated sctools to support the single-nuclei parameter (counting_mode = sn_rna) * Added tests for running the workflow when counting_mode = sn_rna From 1bd9bdc046c2edc54083ba64d501dd39e6c2de76 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 11:39:33 -0400 Subject: [PATCH 5/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index d44a4c6b5..72724878a 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -2,17 +2,11 @@ 2020-04-24 (Date of Last Commit) * Added a new counting_mode parameter to Optimus workflow which enables processing of single-nuclei datasets - * Updated Drop-seq tools to v2.3.0; this update is only used when the workflow is set to the single-nuclei mode (counting_mode = sn_rna) - * Updated sctools to support the single-nuclei parameter (counting_mode = sn_rna) - * Added tests for running the workflow when counting_mode = sn_rna - * Updated the Zarr and Loom output to include a global attribute describing the counting mode - * Added new example datasets that can be used with the Optimus workflow - * Updated the README documentation to detail the new counting_mode parameter, describe example datasets, and to include a new FAQ section @@ -29,11 +23,8 @@ 2019-11-08 (Date of Last Commit) * Addition of support for V3 chemistry - * Addition of input parameter validation step - * Greatly improved documentation - * Improvements to ZARR output # optimus_v1.3.6 @@ -41,13 +32,9 @@ 2019-09-23 (Date of Last Commit) * EmptyDrops output is now included in the ZARR output - * The GTF modification step is removed from the scatter, resulting in better performance and caching - * Memory of several tasks is increased - * The ZARR output is now compulsory and the relevant input flag has been removed - * Support for loom format has been added and a new optional flag dictates if the file is created Documentation has been updated @@ -69,7 +56,6 @@ Documentation has been updated 2019-08-08 (Date of Last Commit) * Release a new patch version of Optimus with an ambitious memory allocation for CalculateCellMetrics task. - * This version and all future versions have been scientifically validated on Mouse reference version mm10 (GRCm39, Gencode M21) # optimus_v1.3.2 From bcc73a363144075fa8e553eff534aa728fd1dd54 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Fri, 24 Apr 2020 11:39:51 -0400 Subject: [PATCH 6/6] Update Optimus.changelog.md --- pipelines/optimus/Optimus.changelog.md | 1 - 1 file changed, 1 deletion(-) diff --git a/pipelines/optimus/Optimus.changelog.md b/pipelines/optimus/Optimus.changelog.md index 72724878a..8419f27cf 100644 --- a/pipelines/optimus/Optimus.changelog.md +++ b/pipelines/optimus/Optimus.changelog.md @@ -15,7 +15,6 @@ 2020-02-28 (Date of Last Commit) * Fixed bug that resulted in emptyDrops output being incorrect - * Updated workflow to WDL 1.0 # optimus_v1.4.0