From c56468c9749c18113bce00b8343d404d4147a337 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Thu, 18 Jul 2024 14:06:49 -0400 Subject: [PATCH 1/3] fixed WARP contact --- website/blog/2021-11-09-blog1.md | 2 +- website/docs/About_WARP/TestingPipelines.md | 2 +- website/docs/Pipelines/ATAC/README.md | 2 +- website/docs/Pipelines/BuildIndices_Pipeline/README.md | 6 +++--- website/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md | 6 +++--- .../Exome_Germline_Single_Sample_Pipeline/README.md | 2 +- .../Genomic_Data_Commons_Whole_Genome_Somatic/README.md | 4 ++-- .../Pipelines/Illumina_Genotyping_Arrays_Pipeline/README.md | 4 ++-- website/docs/Pipelines/Imputation_Pipeline/README.md | 4 ++-- website/docs/Pipelines/JointGenotyping/README.md | 4 ++-- website/docs/Pipelines/Multiome_Pipeline/README.md | 6 +++--- website/docs/Pipelines/Optimus_Pipeline/README.md | 6 +++--- website/docs/Pipelines/PairedTag_Pipeline/README.md | 6 +++--- website/docs/Pipelines/RNA_with_UMIs_Pipeline/README.md | 4 ++-- .../docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md | 6 +++--- website/docs/Pipelines/SlideSeq_Pipeline/README.md | 6 +++--- .../Pipelines/Smart-seq2_Multi_Sample_Pipeline/README.md | 6 +++--- .../README.md | 6 +++--- .../Pipelines/Smart-seq2_Single_Sample_Pipeline/README.md | 6 +++--- .../README.md | 4 ++-- .../Whole_Genome_Germline_Single_Sample_Pipeline/README.md | 4 ++-- website/docs/Pipelines/snM3C/README.md | 6 +++--- website/docs/contribution/README.md | 2 +- .../contribute_to_warp/contribution-guidelines.md | 2 +- .../contribute_to_warp/contribution-tutorial.md | 2 +- website/docs/get-started.md | 2 +- 26 files changed, 55 insertions(+), 55 deletions(-) diff --git a/website/blog/2021-11-09-blog1.md b/website/blog/2021-11-09-blog1.md index e564efcd64..06a63c9e22 100644 --- a/website/blog/2021-11-09-blog1.md +++ b/website/blog/2021-11-09-blog1.md @@ -40,7 +40,7 @@ We recognize that some researchers might want to perform reblocking independent If you’re curious as to whether your WARP pipeline output is a reblocked GVCF, just look at the filename suffix; a reblocked GVCF will have the `.rb.g.vcf` ending. -As always, if you have any questions about working with the updated workflows, [file an issue in WARP](https://github.com/broadinstitute/warp/issues) or reach out to [the WARP team](mailto:warp-pipelines-help@broadinstitute.org ). +As always, if you have any questions about working with the updated workflows, [file an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Additional resources Learn more about the reblocking tool on the [GATK Support website](https://gatk.broadinstitute.org/hc/en-us/articles/4405443600667). diff --git a/website/docs/About_WARP/TestingPipelines.md b/website/docs/About_WARP/TestingPipelines.md index 33e8f47752..50acc66fe0 100644 --- a/website/docs/About_WARP/TestingPipelines.md +++ b/website/docs/About_WARP/TestingPipelines.md @@ -27,4 +27,4 @@ A PR will initiate a pipeline test if it contains changes to the main workflow W ## Contact us with questions about testing -If you have questions about the WARP testing process, please reach out to [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If you have questions about the WARP testing process, please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). diff --git a/website/docs/Pipelines/ATAC/README.md b/website/docs/Pipelines/ATAC/README.md index 06989e960f..b8fc983051 100644 --- a/website/docs/Pipelines/ATAC/README.md +++ b/website/docs/Pipelines/ATAC/README.md @@ -8,7 +8,7 @@ slug: /Pipelines/ATAC/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [2.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [2.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the ATAC workflow diff --git a/website/docs/Pipelines/BuildIndices_Pipeline/README.md b/website/docs/Pipelines/BuildIndices_Pipeline/README.md index 0d0431edc4..547975b821 100644 --- a/website/docs/Pipelines/BuildIndices_Pipeline/README.md +++ b/website/docs/Pipelines/BuildIndices_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/BuildIndices_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [BuildIndices_v3.0.0](https://github.com/broadinstitute/warp/releases) | December, 2023 | Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) | +| [BuildIndices_v3.0.0](https://github.com/broadinstitute/warp/releases) | December, 2023 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![BuildIndices_diagram](./buildindices_diagram.png) @@ -121,8 +121,8 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia support This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN). -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Feedback -Please help us make our tools better by contacting the [WARP Pipelines Team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. \ No newline at end of file +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues) for pipeline-related suggestions or questions. \ No newline at end of file diff --git a/website/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md b/website/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md index 5dac529f8d..3490791d4c 100644 --- a/website/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md +++ b/website/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/CEMBA_MethylC_Seq_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [CEMBA_v1.1.6](https://github.com/broadinstitute/warp/releases) | December, 2023 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [CEMBA_v1.1.6](https://github.com/broadinstitute/warp/releases) | December, 2023 | Elizabeth Kiernan| Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![CEMBA](./CEMBA.png) @@ -190,11 +190,11 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia Support This pipeline is supported and used by the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN). -If your organization also uses this pipeline, we would love to list you! Please reach out to us by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would love to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Have Suggestions? -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md b/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md index 204e4f34af..3566d6b125 100644 --- a/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Exome_Germline_Single_Sample_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [ExomeGermlineSingleSample_v3.1.19](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | March, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [ExomeGermlineSingleSample_v3.1.19](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | March, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | The Exome Germline Single Sample pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data. diff --git a/website/docs/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README.md b/website/docs/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README.md index d3151c4060..b7229e55ba 100644 --- a/website/docs/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README.md +++ b/website/docs/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [GDCWholeGenomeSomaticSingleSample_v1.3.1](https://github.com/broadinstitute/warp/releases) | January, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [GDCWholeGenomeSomaticSingleSample_v1.3.1](https://github.com/broadinstitute/warp/releases) | January, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the GDC Whole Genome Somatic Single Sample pipeline @@ -121,7 +121,7 @@ If you use the GDC Pipeline in your research, please consider citing our preprin Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1 ## Contact us -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. ## Licensing diff --git a/website/docs/Pipelines/Illumina_Genotyping_Arrays_Pipeline/README.md b/website/docs/Pipelines/Illumina_Genotyping_Arrays_Pipeline/README.md index d4c09e7a6d..42abc3d354 100644 --- a/website/docs/Pipelines/Illumina_Genotyping_Arrays_Pipeline/README.md +++ b/website/docs/Pipelines/Illumina_Genotyping_Arrays_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Illumina_Genotyping_Arrays_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [Version 1.12.17](https://github.com/broadinstitute/warp/releases) | March, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [Version 1.12.17](https://github.com/broadinstitute/warp/releases) | March, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![The Illumina Genotyping Array Pipeline](./IlluminaGenotyping.png) @@ -245,7 +245,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Feedback and questions -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Imputation_Pipeline/README.md b/website/docs/Pipelines/Imputation_Pipeline/README.md index 4c8faa68cc..e68d937fd5 100644 --- a/website/docs/Pipelines/Imputation_Pipeline/README.md +++ b/website/docs/Pipelines/Imputation_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Imputation_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [Imputation_v1.1.12](https://github.com/broadinstitute/warp/releases?q=Imputation_v1.0.0&expanded=true) | February, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [Imputation_v1.1.12](https://github.com/broadinstitute/warp/releases?q=Imputation_v1.0.0&expanded=true) | February, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the Imputation pipeline The Imputation pipeline imputes missing genotypes from either a multi-sample VCF or an array of single sample VCFs using a large genomic reference panel. It is based on the [Michigan Imputation Server pipeline](https://imputationserver.readthedocs.io/en/latest/pipeline/). Overall, the pipeline filters, phases, and performs imputation on a multi-sample VCF. It outputs the imputed VCF along with key imputation metrics. @@ -147,7 +147,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Contact us -Help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. ## Licensing diff --git a/website/docs/Pipelines/JointGenotyping/README.md b/website/docs/Pipelines/JointGenotyping/README.md index 6b8aa181ed..9cae9e2916 100644 --- a/website/docs/Pipelines/JointGenotyping/README.md +++ b/website/docs/Pipelines/JointGenotyping/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/JointGenotyping_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [JointGenotyping_v1.6.10](https://github.com/broadinstitute/warp/releases) | February, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in WARP or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) | +| [JointGenotyping_v1.6.10](https://github.com/broadinstitute/warp/releases) | February, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the JointGenotyping workflow @@ -246,4 +246,4 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Feedback -Please help us make our tools better by contacting the [WARP Pipelines Team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. \ No newline at end of file +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. \ No newline at end of file diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index bfe793457a..f0a48497ed 100644 --- a/website/docs/Pipelines/Multiome_Pipeline/README.md +++ b/website/docs/Pipelines/Multiome_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [Multiome v5.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org) | +| [Multiome v5.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![Multiome_diagram](./multiome_diagram.png) @@ -151,11 +151,11 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia support This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN). -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Acknowledgements We are immensely grateful to the members of the BRAIN Initiative (BICAN Sequencing Working Group) and SCORCH for their invaluable and exceptional contributions to this pipeline. Our heartfelt appreciation goes to Alex Dobin, Aparna Bhaduri, Alec Wysoker, Anish Chakka, Brian Herb, Daofeng Li, Fenna Krienen, Guo-Long Zuo, Jeff Goldy, Kai Zhang, Khalid Shakir, Bo Li, Mariano Gabitto, Michael DeBerardine, Mengyi Song, Melissa Goldman, Nelson Johansen, James Nemesh, and Theresa Hodges for their unwavering dedication and remarkable efforts. ## Feedback -Please help us make our tools better by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md index d9b6fccd5d..7c24c22802 100644 --- a/website/docs/Pipelines/Optimus_Pipeline/README.md +++ b/website/docs/Pipelines/Optimus_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Optimus_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [optimus_v7.1.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [optimus_v7.1.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) | ![Optimus_diagram](Optimus_diagram.png) @@ -304,11 +304,11 @@ This pipeline is supported and used by the [Human Cell Atlas](https://www.humanc Each consortium may use slightly different reference files for data analysis or have different post-processing steps. Learn more by reading the [Consortia Processing](./consortia-processing.md) overview. -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Feedback -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. ## Acknowledgements We are immensely grateful to the members of the [Human Cell Atlas Data Coordination Platform](https://data.humancellatlas.org/), BRAIN Initiative ([BICAN](https://brainblog.nih.gov/brain-blog/brain-issues-suite-funding-opportunities-advance-brain-cell-atlases-through-centers) Sequencing Working Group) and [SCORCH](https://nida.nih.gov/about-nida/organization/divisions/division-neuroscience-behavior-dnb/basic-research-hiv-substance-use-disorder/scorch-program) for their invaluable and exceptional contributions to this pipeline. Our heartfelt appreciation goes to Alex Dobin, Aparna Bhaduri, Alec Wysoker, Anish Chakka, Brian Herb, Daofeng Li, Fenna Krienen, Guo-Long Zuo, Jeff Goldy, Kai Zhang, Khalid Shakir, Bo Li, Mariano Gabitto, Michael DeBerardine, Mengyi Song, Melissa Goldman, Nelson Johansen, James Nemesh, and Theresa Hodges for their unwavering dedication and remarkable efforts. diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index a203d53447..c385d90aeb 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/PairedTag_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | |:---:| :---: | :---: | :---: | -| [PairedTag_v1.0.1](https://github.com/broadinstitute/warp/releases) | June, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) | +| [PairedTag_v1.0.1](https://github.com/broadinstitute/warp/releases) | June, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the Paired-Tag workflow @@ -141,7 +141,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia support This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN). -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Acknowledgements @@ -150,4 +150,4 @@ We are immensely grateful to the members of the BRAIN Initiative (BICAN Sequenci ## Feedback -Please help us make our tools better by contacting the [WARP Pipelines Team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. \ No newline at end of file +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. \ No newline at end of file diff --git a/website/docs/Pipelines/RNA_with_UMIs_Pipeline/README.md b/website/docs/Pipelines/RNA_with_UMIs_Pipeline/README.md index 2c7b1f08ca..1a5e9fce3d 100644 --- a/website/docs/Pipelines/RNA_with_UMIs_Pipeline/README.md +++ b/website/docs/Pipelines/RNA_with_UMIs_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/RNA_with_UMIs_Pipeline/README | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [RNAWithUMIsPipeline_v1.0.16](https://github.com/broadinstitute/warp/releases?q=RNAwithUMIs&expanded=true) | February, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) & [Kaylee Mathews](mailto:kmathews@broadinstitute.org)| Please file GitHub issues in warp or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [RNAWithUMIsPipeline_v1.0.16](https://github.com/broadinstitute/warp/releases?q=RNAwithUMIs&expanded=true) | February, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![RNAWithUMIs_diagram](rna-with-umis_diagram.png) @@ -274,6 +274,6 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Feedback -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. \ No newline at end of file diff --git a/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md b/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md index 2d5aaba902..0512f9290a 100644 --- a/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md +++ b/website/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Single_Cell_ATAC_Seq_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [scATAC 1.3.2](https://github.com/broadinstitute/warp/releases) | May 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [scATAC 1.3.2](https://github.com/broadinstitute/warp/releases) | May 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![scATAC_diagram](./scATAC_diagram.png) @@ -170,8 +170,8 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia Support This pipeline is supported and used by the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN). -If your organization also uses this pipeline, we would love to list you! Please reach out to us by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would love to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Pipeline Improvements -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/SlideSeq_Pipeline/README.md b/website/docs/Pipelines/SlideSeq_Pipeline/README.md index 43fa967859..b9cd1d3def 100644 --- a/website/docs/Pipelines/SlideSeq_Pipeline/README.md +++ b/website/docs/Pipelines/SlideSeq_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/SlideSeq_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [SlideSeq v3.1.6](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:warp-pipelines-help@broadinstitute.org) | +| [SlideSeq v3.1.6](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![SlideSeq_diagram](./slide-seq_diagram.png) @@ -235,8 +235,8 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia support This pipeline is supported by the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN) and BRAIN Initiative Cell Atlas Network (BICAN). -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting the [WARP Pipelines team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Feedback -Please help us make our tools better by contacting the [WARP Pipelines Team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README.md b/website/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README.md index 1a6368c014..8548f77fe6 100644 --- a/website/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Smart-seq2_Multi_Sample_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [MultiSampleSmartSeq2_v2.2.21](https://github.com/broadinstitute/warp/releases) | December, 2023 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [MultiSampleSmartSeq2_v2.2.21](https://github.com/broadinstitute/warp/releases) | December, 2023 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction @@ -110,9 +110,9 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia Support This pipeline is supported and used by the [Human Cell Atlas](https://www.humancellatlas.org/) (HCA) project. -If your organization also uses this pipeline, we would love to list you! Please reach out to us by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would love to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Have Suggestions? -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md index 909dfe887e..ea1f81efae 100644 --- a/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [MultiSampleSmartSeq2SingleNuclei_v1.3.4](https://github.com/broadinstitute/warp/releases) | May, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [MultiSampleSmartSeq2SingleNuclei_v1.3.4](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![](./snSS2.png) @@ -192,7 +192,7 @@ This pipeline is supported and used by the [BRAIN Initiative Cell Census Network Each consortia may use slightly different reference files for data analysis or have different post-processing steps. Learn more by reading the [Consortia Processing](./consortia-processing.md) overview. -If your organization also uses this pipeline, we would love to list you! Please reach out to us by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would love to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Feedback -Please help us make our tools better by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README.md b/website/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README.md index 214484949e..b6fd9b967f 100644 --- a/website/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Smart-seq2_Single_Sample_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [smartseq2_v5.1.20](https://github.com/broadinstitute/warp/releases) | February, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [smartseq2_v5.1.20](https://github.com/broadinstitute/warp/releases) | February, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![](./smartseq_image.png) @@ -223,7 +223,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia Support This pipeline is supported and used by the [Human Cell Atlas](https://www.humancellatlas.org/) (HCA) project. -If your organization also uses this pipeline, we would love to list you! Please reach out to us by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would love to list you! Please [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Have Suggestions? -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md b/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md index 6e4689eea4..a41f270a53 100644 --- a/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md +++ b/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [UltimaGenomicsWholeGenomeGermline_v1.0.16](https://github.com/broadinstitute/warp/releases) | March, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) & [Kaylee Mathews](mailto:kmathews@broadinstitute.org)| Please file GitHub issues in warp or contact [the wARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| [UltimaGenomicsWholeGenomeGermline_v1.0.16](https://github.com/broadinstitute/warp/releases) | March, 2024 | Elizabeth Kiernan & Kaylee Mathews| Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![UG_diagram](ug_diagram.png) @@ -280,7 +280,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Feedback -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. diff --git a/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md b/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md index ed38b4bdf2..9fec00e7e5 100644 --- a/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md +++ b/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| WholeGenomeGermlineSingleSample_v3.1.20 (see [releases page](https://github.com/broadinstitute/warp/releases)) | March, 2024 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) | +| WholeGenomeGermlineSingleSample_v3.1.20 (see [releases page](https://github.com/broadinstitute/warp/releases)) | March, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the Whole Genome Germline Single Sample Pipeline The Whole Genome Germline Single Sample (WGS) pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human whole-genome sequencing data. It includes the DRAGEN-GATK mode, which makes the pipeline functionally equivalent to DRAGEN’s analysis pipeline (read more in this [DRAGEN-GATK blog](https://gatk.broadinstitute.org/hc/en-us/articles/360039984151)). @@ -377,7 +377,7 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Contact us -Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions. +Please help us make our tools better by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues); we welcome pipeline-related suggestions or questions. ## Licensing diff --git a/website/docs/Pipelines/snM3C/README.md b/website/docs/Pipelines/snM3C/README.md index 7d48aebe13..776494d5a7 100644 --- a/website/docs/Pipelines/snM3C/README.md +++ b/website/docs/Pipelines/snM3C/README.md @@ -6,7 +6,7 @@ slug: /Pipelines/snm3C/README | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [snm3C_v4.0.0](https://github.com/broadinstitute/warp/releases) | March, 2024 | [Kaylee Mathews](mailto:warp-pipelines-help@broadinsitute.org) | Please file GitHub issues in the [WARP repository](https://github.com/broadinstitute/warp/issues) | +| [snm3C_v4.0.0](https://github.com/broadinstitute/warp/releases) | March, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to snm3C @@ -180,11 +180,11 @@ Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konw ## Consortia support This pipeline is supported by the [BRAIN Initiative](https://braininitiative.nih.gov/) (BICCN and BICAN). -If your organization also uses this pipeline, we would like to list you! Please reach out to us by contacting the [WARP Pipeline Development team](mailto:warp-pipelines-help@broadinstitute.org). +If your organization also uses this pipeline, we would like to list you! Please reach out to us by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). ## Acknowledgements We are immensely grateful to the members of the BRAIN Initiative ([BICAN](https://brainblog.nih.gov/brain-blog/brain-issues-suite-funding-opportunities-advance-brain-cell-atlases-through-centers) Sequencing Working Group) and [SCORCH](https://nida.nih.gov/about-nida/organization/divisions/division-neuroscience-behavior-dnb/basic-research-hiv-substance-use-disorder/scorch-program) for their invaluable and exceptional contributions to this pipeline. Our heartfelt appreciation goes to our collaborators and the developers of these tools, Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker. ## Feedback -For questions, suggestions, or feedback related to the snm3C pipeline, please contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). Your feedback is valuable for improving the pipeline and addressing any issues that may arise during its usage. +For questions, suggestions, or feedback related to the snm3C pipeline, please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). Your feedback is valuable for improving the pipeline and addressing any issues that may arise during its usage. diff --git a/website/docs/contribution/README.md b/website/docs/contribution/README.md index d364edd989..82e602b310 100755 --- a/website/docs/contribution/README.md +++ b/website/docs/contribution/README.md @@ -9,7 +9,7 @@ Welcome to WARP! We really appreciate your contribution! Please take some time t You can contribute to the code for WARP pipelines or to the WARP documentation. In this Contribution section, you will find guides relating to both types of updates. More guides will be added as we develop them. -You can also make suggestions relating to WARP pipelines by filing an issue in [GitHub](https://github.com/broadinstitute/warp) or by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +You can also make suggestions relating to WARP pipelines by [filing an issue in WARP](https://github.com/broadinstitute/warp/issues). To leave feedback or suggest changes for WARP documentation, you can use the `Feedback` icon to the right of each WARP website page. After rating your experience, a text box will be available to request specific changes. diff --git a/website/docs/contribution/contribute_to_warp/contribution-guidelines.md b/website/docs/contribution/contribute_to_warp/contribution-guidelines.md index 37dc92ddf0..02b905fc72 100644 --- a/website/docs/contribution/contribute_to_warp/contribution-guidelines.md +++ b/website/docs/contribution/contribute_to_warp/contribution-guidelines.md @@ -88,4 +88,4 @@ All pipelines must pass syntax, scientific and Smart-tests, as described in the To learn more about how to apply these contribution guidelines to an example small pipeline update, see the [Example Contribution](./contribution-tutorial.md). ## Still have questions? -Contact us by [filing an issue](https://github.com/broadinstitute/warp/issues/new) or email [the WARP team](mailto:warp-pipelines-help@broadinstitute.org). +Contact us by [filing an issue](https://github.com/broadinstitute/warp/issues/new). diff --git a/website/docs/contribution/contribute_to_warp/contribution-tutorial.md b/website/docs/contribution/contribute_to_warp/contribution-tutorial.md index 7b965e30be..209bfd9e80 100644 --- a/website/docs/contribution/contribute_to_warp/contribution-tutorial.md +++ b/website/docs/contribution/contribute_to_warp/contribution-tutorial.md @@ -83,4 +83,4 @@ Once our updates are merged to the **master** branch, the pipeline will be relea ## Have questions? -Contact us by [filing an issue](https://github.com/broadinstitute/warp/issues/new) or email [the WARP team](mailto:warp-pipelines-help@broadinstitute.org ). +Contact us by [filing an issue](https://github.com/broadinstitute/warp/issues/new). diff --git a/website/docs/get-started.md b/website/docs/get-started.md index 0c6a77bc70..25b7520991 100755 --- a/website/docs/get-started.md +++ b/website/docs/get-started.md @@ -88,7 +88,7 @@ Each pipeline in WARP has accompanying continuous integration tests that run on ## Feedback -WARP is always evolving! Please file any issues in GitHub or contact [the WARP Team](mailto:warp-pipelines-help@broadinstitute.org) with suggestions, feedback, or questions. We are always excited to discuss cloud data processing, provenance and reproducibility in scientific analysis, new pipeline features, or potential collaborations. Don’t hesitate to reach out! +WARP is always evolving! Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) with suggestions, feedback, or questions. We are always excited to discuss cloud data processing, provenance and reproducibility in scientific analysis, new pipeline features, or potential collaborations. Don’t hesitate to reach out! Our planned upcoming improvements include: From 42e461c80988c7da50fe426a93d668a24ff27e7f Mon Sep 17 00:00:00 2001 From: ekiernan Date: Thu, 18 Jul 2024 14:20:56 -0400 Subject: [PATCH 2/3] updated doc versions --- .../Pipelines/Multiome_Pipeline/README.md | 26 +++++++++---------- .../Optimus_Pipeline/Library-metrics.md | 2 +- .../docs/Pipelines/Optimus_Pipeline/README.md | 7 ++++- .../Pipelines/PairedTag_Pipeline/README.md | 5 ++-- website/docs/Pipelines/snM3C/README.md | 2 +- 5 files changed, 24 insertions(+), 18 deletions(-) diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index f0a48497ed..3a22bff060 100644 --- a/website/docs/Pipelines/Multiome_Pipeline/README.md +++ b/website/docs/Pipelines/Multiome_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [Multiome v5.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [Multiome v5.1.0](https://github.com/broadinstitute/warp/releases) | July, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![Multiome_diagram](./multiome_diagram.png) @@ -68,18 +68,18 @@ Multiome can be deployed using [Cromwell](https://cromwell.readthedocs.io/en/sta | emptydrops_lower | Optional threshold for UMIs for the Optimus (GEX) pipeline that empty drops tool should consider for determining cell; data below threshold is not removed; default is "100". | Integer | | force_no_check | Optional boolean for the Optimus (GEX) pipeline indicating if the pipeline should perform checks; default is "false". | Boolean | | ignore_r1_read_length | Optional boolean for the Optimus (GEX) pipeline indicating if the pipeline should ignore barcode chemistry check; if "true", the workflow will not ensure the `10x_chemistry_version` input matches the chemistry in the read 1 FASTQ; default is "false". | Boolean | -| star_strand_mode | Optional string for the Optimus (GEX) pipeline for performing STARsolo alignment on forward stranded, reverse stranded, or unstranded data; default is "Forward". | String | -| count_exons | Optional boolean for the Optimus (GEX) pipeline indicating if the workflow should calculate exon counts **when in single-nucleus (sn_rna) mode**; if "true" in sc_rna mode, the workflow will return an error; default is "false". | Boolean | -| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag. | String | -| atac_r1_fastq | Array of read 1 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] | -| atac_r2_fastq | Array of barcodes FASTQ files representing a single 10x multiome ATAC library. | Array[File] | -| atac_r3_fastq | Array of read 2 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] | -| tar_bwa_reference | TAR file containing the reference index files for BWA-mem alignment for the ATAC pipeline. | File | -| chrom_sizes | File containing the genome chromosome sizes; used to calculate ATAC fragment file metrics. | File | -| adapter_seq_read1 | Optional string describing the adapter sequence for ATAC read 1 paired-end reads to be used during adapter trimming with Cutadapt; default is "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG". | String | -| adapter_seq_read3 | Optional string describing the adapter sequence for ATAC read 2 paired-end reads to be used during adapter trimming with Cutadapt; default is "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG". | String | -| run_cellbender | Optional boolean used to determine if the Optimus (GEX) pipeline should run CellBender on the output gene expression h5ad file, `h5ad_output_file_gex`; default is "false". | Boolean | -| vm_size | String defining the Azure virtual machine family for the workflow (default: "Standard_M128s"). | String | +| star_strand_mode | Optional string for the Optimus (GEX) pipeline for performing STARsolo alignment on forward stranded, reverse stranded, or unstranded data; default is "Forward". | String | +| count_exons | Optional boolean for the Optimus (GEX) pipeline indicating if the workflow should calculate exon counts **when in single-nucleus (sn_rna) mode**; if "true" in sc_rna mode, the workflow will return an error; default is "false". | Boolean | +| soloMultiMappers | Optional string describing whether or not the Optimus (GEX) pipeline should run STARsolo with the `--soloMultiMappers` flag. | String | +| atac_r1_fastq | Array of read 1 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] | +| atac_r2_fastq | Array of barcodes FASTQ files representing a single 10x multiome ATAC library. | Array[File] | +| atac_r3_fastq | Array of read 2 paired-end FASTQ files representing a single 10x multiome ATAC library. | Array[File] | +| tar_bwa_reference | TAR file containing the reference index files for BWA-mem alignment for the ATAC pipeline. | File | +| chrom_sizes | File containing the genome chromosome sizes; used to calculate ATAC fragment file metrics. | File | +| adapter_seq_read1 | Optional string describing the adapter sequence for ATAC read 1 paired-end reads to be used during adapter trimming with Cutadapt; default is "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG". | String | +| adapter_seq_read3 | Optional string describing the adapter sequence for ATAC read 2 paired-end reads to be used during adapter trimming with Cutadapt; default is "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG". | String | +| run_cellbender | Optional boolean used to determine if the Optimus (GEX) pipeline should run CellBender on the output gene expression h5ad file, `h5ad_output_file_gex`; default is "false". | Boolean | +| vm_size | String defining the Azure virtual machine family for the workflow (default: "Standard_M128s"). | String | #### Sample inputs for analyses in a Terra Workspace diff --git a/website/docs/Pipelines/Optimus_Pipeline/Library-metrics.md b/website/docs/Pipelines/Optimus_Pipeline/Library-metrics.md index 46f0811b7d..cc704eace8 100644 --- a/website/docs/Pipelines/Optimus_Pipeline/Library-metrics.md +++ b/website/docs/Pipelines/Optimus_Pipeline/Library-metrics.md @@ -4,7 +4,7 @@ sidebar_position: 5 # Optimus Library-level metrics -The following table describes the library level metrics of the produced by the Optimus workflow. These are calcuated using custom python scripts available in the warp-tools repository. The Optimus workflow aligns files in shards to parallelize computationally intensive steps. This results in multiple matrix market files and shard-levl library metrics. +The following table describes the library level metrics of the produced by the Optimus workflow. These are calcuated using custom python scripts available in the warp-tools repository. The Optimus workflow aligns files in shards to parallelize computationally intensive steps. This results in multiple matrix market files and shard-level library metrics. To produce the library-level metrics here, the [combined_mtx.py script](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/star-merge-npz/scripts/combined_mtx.py) combines all the shard-level matrix market files into one raw mtx file. Then, STARsolo is run to filter this matrix to only those barcodes that meet STARsolo's criteria of cells (using the Emptydrops_CR parameter). Lastly, the [combine_shard_metrics.py script](https://github.com/broadinstitute/warp-tools/blob/develop/3rd-party-tools/star-merge-npz/scripts/combine_shard_metrics.py) uses the filtered matrix and the all of the shard-level metrics files produced by STARsolo to calculate the metrics below. Each of the scripts are called from [MergeStarOutput task](https://github.com/broadinstitute/warp/blob/develop/tasks/skylab/StarAlign.wdl) of the Optimus workflow. diff --git a/website/docs/Pipelines/Optimus_Pipeline/README.md b/website/docs/Pipelines/Optimus_Pipeline/README.md index 7c24c22802..82c686d341 100644 --- a/website/docs/Pipelines/Optimus_Pipeline/README.md +++ b/website/docs/Pipelines/Optimus_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/Optimus_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [optimus_v7.1.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) | +| [optimus_v7.2.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | July, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues) | ![Optimus_diagram](Optimus_diagram.png) @@ -370,4 +370,9 @@ Unlike Cell Ranger references, Optimus references are downloaded directly from G In the case of multi-mapped pseudogenes, Optimus and Cell Ranger will produce different results. Optimus does not count multi-mapped reads in the final count matrix, whereas Cell Ranger will keep potential multi-mapped reads because it does not identify the pseudogene reads. ::: +:::note Question How does estimated cells differ between Cell Ranger and Optimus? + +Overall, the estimated cells produced by Optimus and Cell Ranger should only slightly vary. However, if you are using Optimus in the Multiome pipeline and trying to compare estimated cells to Cell Ranger ARC, you might find that ARC calls fewer cells. This is because ARC sets a threshold that both the ATAC and gene expression cells must pass, whereas Optimus is only setting a threshold for the gene expression side of the pipeline. +::: + diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index c385d90aeb..b71987ef33 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -7,7 +7,7 @@ slug: /Pipelines/PairedTag_Pipeline/README | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback | |:---:| :---: | :---: | :---: | -| [PairedTag_v1.0.1](https://github.com/broadinstitute/warp/releases) | June, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [PairedTag_v1.1.0](https://github.com/broadinstitute/warp/releases) | July, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the Paired-Tag workflow @@ -60,6 +60,7 @@ The Paired-Tag workflow inputs are specified in JSON configuration files. Exampl | Parameter name | Description | Type | | --- | --- | --- | | input_id | Unique identifier describing the biological sample or replicate that corresponds with the FASTQ files; can be a human-readable name or UUID. | String | +| nash_id | Optional identifier that can be used to demarcate the library aliquot or sample. | | counting_mode | Optional string that determines whether the Optimus (GEX) pipeline should be run in single-cell mode (sc_rna) or single-nucleus mode (sn_rna); default is "sn_rna". | String | | gex_r1_fastq | Array of read 1 FASTQ files representing a single GEX 10x library. | Array[File] | | gex_r2_fastq | Array of read 2 FASTQ files representing a single GEX 10x library.| Array[File] | @@ -115,7 +116,7 @@ The Paired-Tag workflow calls two WARP subworkflows and an additional task which | gene_metrics_gex | `_gex.gene_metrics.csv.gz` | CSV file containing the per-gene metrics. | | cell_calls_gex | `_gex.emptyDrops` | TSV file containing the EmptyDrops results when the Optimus workflow is run in sc_rna mode. | | h5ad_output_file_gex | `_gex.h5ad` | h5ad (Anndata) file containing the raw cell-by-gene count matrix, gene metrics, cell metrics, and global attributes. See the [Optimus Count Matrix Overview](../Optimus_Pipeline/Loom_schema.md) for more details. | -| library_metrics | `_library_metrics.csv` | Optional CSV file containing all library-level metrics calculated with STARsolo for gene expression data. | +| library_metrics | `__library_metrics.csv` | Optional CSV file containing all library-level metrics calculated with STARsolo for gene expression data. | | cloud_provider | String describing the cloud provider that should be used to run the workflow; value should be "gcp" or "azure". | String | | multimappers_EM_matrix | `UniqueAndMult-EM.mtx` | Optional output produced when `soloMultiMappers` is "EM"; see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| | multimappers_Uniform_matrix | `UniqueAndMult-Uniform.mtx` | Optional output produced when `soloMultiMappers` is "Uniform" (default); see STARsolo [documentation](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#multi-gene-reads) for more information.| diff --git a/website/docs/Pipelines/snM3C/README.md b/website/docs/Pipelines/snM3C/README.md index 776494d5a7..fe5e0fa2f9 100644 --- a/website/docs/Pipelines/snM3C/README.md +++ b/website/docs/Pipelines/snM3C/README.md @@ -6,7 +6,7 @@ slug: /Pipelines/snm3C/README | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback | | :----: | :---: | :----: | :--------------: | -| [snm3C_v4.0.0](https://github.com/broadinstitute/warp/releases) | March, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [snm3C_v4.0.1](https://github.com/broadinstitute/warp/releases) | March, 2024 | Kaylee Mathews | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to snm3C From 1bf735de1bf3ddc258e83965b1c98b8a6d0f1d53 Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Thu, 18 Jul 2024 14:30:19 -0400 Subject: [PATCH 3/3] Update website/docs/Pipelines/PairedTag_Pipeline/README.md Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> --- website/docs/Pipelines/PairedTag_Pipeline/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index b71987ef33..7baa235e50 100644 --- a/website/docs/Pipelines/PairedTag_Pipeline/README.md +++ b/website/docs/Pipelines/PairedTag_Pipeline/README.md @@ -60,7 +60,7 @@ The Paired-Tag workflow inputs are specified in JSON configuration files. Exampl | Parameter name | Description | Type | | --- | --- | --- | | input_id | Unique identifier describing the biological sample or replicate that corresponds with the FASTQ files; can be a human-readable name or UUID. | String | -| nash_id | Optional identifier that can be used to demarcate the library aliquot or sample. | +| nhash_id | Optional identifier that can be used to demarcate the library aliquot or sample. | | counting_mode | Optional string that determines whether the Optimus (GEX) pipeline should be run in single-cell mode (sc_rna) or single-nucleus mode (sn_rna); default is "sn_rna". | String | | gex_r1_fastq | Array of read 1 FASTQ files representing a single GEX 10x library. | Array[File] | | gex_r2_fastq | Array of read 2 FASTQ files representing a single GEX 10x library.| Array[File] |