From 79d16568008518bb8dbc3300e2a16ffe0737cacf Mon Sep 17 00:00:00 2001 From: ekiernan Date: Tue, 12 Nov 2024 08:53:15 -0500 Subject: [PATCH 1/4] added atac_percent_metrics --- pipelines/skylab/atac/atac.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl index 30cb017ab8..01b5317718 100644 --- a/pipelines/skylab/atac/atac.wdl +++ b/pipelines/skylab/atac/atac.wdl @@ -575,7 +575,7 @@ task CreateFragmentFile { print("Print number of cells", number_of_cells) atac_percent_target = number_of_cells / expected_cells*100 print("Setting percent target in nested dictionary") - data['Cells']['percent_target'] = atac_percent_target + data['Cells']['atac_percent_target'] = atac_percent_target # Flatten the dictionary From 54f451b5f0e0cdae1eb3a9061ec7708fe2ddb403 Mon Sep 17 00:00:00 2001 From: ekiernan Date: Tue, 12 Nov 2024 09:05:19 -0500 Subject: [PATCH 2/4] updated changelogs and readmes --- pipelines/skylab/atac/atac.changelog.md | 6 ++++++ pipelines/skylab/atac/atac.wdl | 2 +- pipelines/skylab/multiome/Multiome.changelog.md | 8 ++++++++ pipelines/skylab/multiome/Multiome.wdl | 2 +- pipelines/skylab/paired_tag/PairedTag.changelog.md | 5 +++++ pipelines/skylab/paired_tag/PairedTag.wdl | 2 +- website/docs/Pipelines/ATAC/README.md | 2 +- website/docs/Pipelines/ATAC/library-metrics.md | 2 +- website/docs/Pipelines/Multiome_Pipeline/README.md | 6 +++--- website/docs/Pipelines/PairedTag_Pipeline/README.md | 2 +- 10 files changed, 28 insertions(+), 9 deletions(-) diff --git a/pipelines/skylab/atac/atac.changelog.md b/pipelines/skylab/atac/atac.changelog.md index 3a8c05fb03..0a32a0f6ee 100644 --- a/pipelines/skylab/atac/atac.changelog.md +++ b/pipelines/skylab/atac/atac.changelog.md @@ -1,7 +1,13 @@ +# 2.5.1 +2024-11-12 (Date of Last Commit) + +* Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools + # 2.5.0 2024-10-23 (Date of Last Commit) * Updated the tabix flag in CreateFragmentFile task to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp +* Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools # 2.4.0 2024-10-23 (Date of Last Commit) diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl index 01b5317718..4e8b0aaf17 100644 --- a/pipelines/skylab/atac/atac.wdl +++ b/pipelines/skylab/atac/atac.wdl @@ -49,7 +49,7 @@ workflow ATAC { String adapter_seq_read3 = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG" } - String pipeline_version = "2.5.0" + String pipeline_version = "2.5.1" # Determine docker prefix based on cloud provider String gcr_docker_prefix = "us.gcr.io/broad-gotc-prod/" diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md index 35ebd07702..3b18e933ff 100644 --- a/pipelines/skylab/multiome/Multiome.changelog.md +++ b/pipelines/skylab/multiome/Multiome.changelog.md @@ -1,7 +1,15 @@ +# 5.9.1 +2024-11-12 (Date of Last Commit) + +* Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools + # 5.9.0 2024-10-21 (Date of Last Commit) + * Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task changes the format for the ATAC fragment file index * Renamed the fragment file index from atac_fragment_tsv_tbi to atac_fragment_tsv_index + + # 5.8.0 2024-10-23 (Date of Last Commit) diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl index 145adbe465..0d291633de 100644 --- a/pipelines/skylab/multiome/Multiome.wdl +++ b/pipelines/skylab/multiome/Multiome.wdl @@ -9,7 +9,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils workflow Multiome { - String pipeline_version = "5.9.0" + String pipeline_version = "5.9.1" input { String cloud_provider diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md index 34e67e5102..e836d03606 100644 --- a/pipelines/skylab/paired_tag/PairedTag.changelog.md +++ b/pipelines/skylab/paired_tag/PairedTag.changelog.md @@ -1,3 +1,8 @@ +# 1.8.2 +2024-11-12 (Date of Last Commit) + +* * Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools + # 1.8.1 2024-11-04 (Date of Last Commit) diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl index 5896f5ae60..155254056a 100644 --- a/pipelines/skylab/paired_tag/PairedTag.wdl +++ b/pipelines/skylab/paired_tag/PairedTag.wdl @@ -8,7 +8,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils workflow PairedTag { - String pipeline_version = "1.8.1" + String pipeline_version = "1.8.2" input { diff --git a/website/docs/Pipelines/ATAC/README.md b/website/docs/Pipelines/ATAC/README.md index ec70252fb1..86d3eaab3e 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 | | :----: | :---: | :----: | :--------------: | -| [2.4.0](https://github.com/broadinstitute/warp/releases) | October, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [2.5.1](https://github.com/broadinstitute/warp/releases) | November, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the ATAC workflow diff --git a/website/docs/Pipelines/ATAC/library-metrics.md b/website/docs/Pipelines/ATAC/library-metrics.md index 3e80bc85e4..6b86005bfe 100644 --- a/website/docs/Pipelines/ATAC/library-metrics.md +++ b/website/docs/Pipelines/ATAC/library-metrics.md @@ -31,6 +31,6 @@ The [ATAC pipeline](README.md) uses [SnapATAC2](https://github.com/kaizhang/Snap | Number_of_peaks | The total number of peaks, or regions of accessible chromatin, identified in the dataset, representing potential regulatory elements. | | fraction_of_genome_in_peaks | The fraction of the genome that is covered by identified peaks, indicating the extent of chromatin accessibility across the genome. | | fraction_of_high-quality_fragments_overlapping_peaks | The fraction of high-quality fragments that overlap with identified peaks, providing an indication of the efficiency of the assay in capturing accessible regions. | -| percent_target | Percent of cells recovered; value is calculated as estimated_cells/expected_cells. | +| atac_percent_target | Percent of cells recovered; value is calculated as estimated_cells/expected_cells. | diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md index 625d3320d7..131a81aca5 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 v5.8.0](https://github.com/broadinstitute/warp/releases) | October, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [Multiome v5.9.1](https://github.com/broadinstitute/warp/releases) | November, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ![Multiome_diagram](./multiome_diagram.png) @@ -108,9 +108,9 @@ The Multiome workflow calls two WARP subworkflows, one external subworkflow (opt | multiome_pipeline_version_out | N.A. | String describing the version of the Multiome pipeline used. | | bam_aligned_output_atac | `_atac.bam` | BAM file containing aligned reads from ATAC workflow. | | fragment_file_atac | `_atac.fragments.sorted.tsv.gz` | Sorted and bgzipped TSV file containing fragment start and stop coordinates per barcode. The columns are "Chromosome", "Start", "Stop", "ATAC Barcode", "Number of reads", and "GEX Barcode". | -| fragment_file_index | `_atac.fragments.sorted.tsv.gz.tbi` | tabix index file for the fragment file. | +| fragment_file_index | `_atac.fragments.sorted.tsv.gz.csi` | Tabix CSI index file for the fragment file. | | snap_metrics_atac | `_atac.metrics.h5ad` | h5ad (Anndata) file containing per-barcode metrics from SnapATAC2. Also contains the equivalent gene expression barcode for each ATAC barcode in the `gex_barcodes` column of the `h5ad.obs` property. See the [ATAC Count Matrix Overview](../ATAC/count-matrix-overview.md) for more details. | -| atac_library_metrics | `_atac_.metrics.csv` | CSV with library-level metrics produced by SnapATAC2. See the ATAC [Library Level Metrics Overview](../ATAC/library-metrics.md) for more details. | +| atac_library_metrics | `_atac__library_metrics.csv` | CSV with library-level metrics produced by SnapATAC2. See the ATAC [Library Level Metrics Overview](../ATAC/library-metrics.md) for more details. | | genomic_reference_version_gex | `.txt` | File containing the Genome build, source and GTF annotation version. | | bam_gex | `_gex.bam` | BAM file containing aligned reads from Optimus workflow. | | matrix_gex | `_gex_sparse_counts.npz` | NPZ file containing raw gene by cell counts. | diff --git a/website/docs/Pipelines/PairedTag_Pipeline/README.md b/website/docs/Pipelines/PairedTag_Pipeline/README.md index 323b3f33b9..394dd4c6a3 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_v1.8.0](https://github.com/broadinstitute/warp/releases) | October, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | +| [PairedTag_v1.8.2](https://github.com/broadinstitute/warp/releases) | November, 2024 | WARP Pipelines | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). | ## Introduction to the Paired-Tag workflow From 8b994c67da40fb5fc3d233ee2539276a8f757543 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 12 Nov 2024 14:06:47 +0000 Subject: [PATCH 3/4] Updated pipeline_versions.txt with all pipeline version information --- pipeline_versions.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index c6f62d8d65..6780e2b78d 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -30,11 +30,11 @@ ExomeReprocessing 3.3.3 2024-11-04 BuildIndices 3.0.0 2023-12-06 scATAC 1.3.2 2023-08-03 snm3C 4.0.4 2024-08-06 -Multiome 5.9.0 2024-10-21 -PairedTag 1.8.1 2024-11-04 +Multiome 5.9.1 2024-11-12 +PairedTag 1.8.2 2024-11-12 MultiSampleSmartSeq2 2.2.22 2024-09-11 MultiSampleSmartSeq2SingleNucleus 2.0.3 2024-11-04 Optimus 7.8.1 2024-11-04 -atac 2.5.0 2024-10-23 +atac 2.5.1 2024-11-12 SmartSeq2SingleSample 5.1.21 2024-09-11 SlideSeq 3.4.4 2024-11-04 From a8d0e0a247cdc04f9a7f23271c42b7fbc128fc4c Mon Sep 17 00:00:00 2001 From: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com> Date: Tue, 12 Nov 2024 09:16:20 -0500 Subject: [PATCH 4/4] Update pipelines/skylab/paired_tag/PairedTag.changelog.md Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> --- pipelines/skylab/paired_tag/PairedTag.changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md index e836d03606..44d0d6fbe4 100644 --- a/pipelines/skylab/paired_tag/PairedTag.changelog.md +++ b/pipelines/skylab/paired_tag/PairedTag.changelog.md @@ -1,7 +1,7 @@ # 1.8.2 2024-11-12 (Date of Last Commit) -* * Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools +* Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools # 1.8.1 2024-11-04 (Date of Last Commit)