Merge branch 'develop' into lk-PD2432-gex-barcodes-to-fragment-file

broadinstitute · Nov 30, 2023 · a1403e5 · a1403e5
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diff --git a/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.14
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.10 ExomeGermlineSingleSample pipeline version
 
 # 3.1.13
 2023-10-10 (Date of Last Commit)

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -2,6 +2,7 @@
 2023-11-21 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.9 UltimaGenomicsWholeGenomeGermline pipeline version
 
 # 1.0.10
 2023-09-18 (Date of Last Commit)

diff --git a/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.15
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.11 WholeGenomeGermlineSingleSample pipeline version
 
 # 3.1.14 
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md
@@ -1,7 +1,8 @@
 # 2.1.13
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 2.1.10 VariantCalling pipeline version
 
 # 2.1.12
 2023-09-18 (Date of Last Commit)

diff --git a/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.11
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.8 UltimaGenomicsWholeGenomeCramOnly pipeline version
 
 # 1.0.10
 2023-09-18 (Date of Last Commit)

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,7 +1,8 @@
 # 1.0.12
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 1.0.9 BroadInternalUltimaGenomics pipeline version
 
 # 1.0.11
 2023-09-18 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.14
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.10 ExomeReprocessing pipeline version
 
 # 3.1.13
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.16
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.12 ExternalExomeReprocessing pipeline version
 
 # 3.1.15
 2023-10-10 (Date of Last Commit)

diff --git a/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 2.1.16
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 2.1.12 ExternalWholeGenomeReprocessing pipeline version
 
 # 2.1.15
 2023-10-10 (Date of Last Commit)

diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md
@@ -1,7 +1,8 @@
 # 3.1.15
-2023-11-21 (Date of Last Commit)
+2023-11-29 (Date of Last Commit)
 
 * Fixed bug in ReblockGVCFs; this does not affect this pipeline.
+* Reverted the VerifyBamID docker image back to the 3.1.11 WholeGenomeReprocessing pipeline version
 
 # 3.1.14
 2023-10-10 (Date of Last Commit)

diff --git a/tasks/broad/BamProcessing.wdl b/tasks/broad/BamProcessing.wdl
@@ -417,9 +417,7 @@ task CheckContamination {
     Float contamination_underestimation_factor
     Boolean disable_sanity_check = false
 
-    # this docker image was built using the commit hash c1cba76e979904eb69c31520a0d7f5be63c72253 (v1.0.6)from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/c1cba76e979904eb69c31520a0d7f5be63c72253
-    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-c1cba76e979904eb69c31520a0d7f5be63c72253-1692099985"
+     String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-c1cba76e979904eb69c31520a0d7f5be63c72253-1639071840"
   }
 
   Int disk_size = ceil(size(input_bam, "GiB") + size(ref_fasta, "GiB")) + 30
@@ -468,8 +466,6 @@ task CheckContamination {
     preemptible: preemptible_tries
     memory: "7.5 GiB"
     disks: "local-disk " + disk_size + " HDD"
-    # this docker image was built using the commit hash c1cba76e979904eb69c31520a0d7f5be63c72253 from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/c1cba76e979904eb69c31520a0d7f5be63c72253
     docker: docker
     cpu: 2
   }

diff --git a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl
@@ -390,9 +390,8 @@ task CheckContamination {
     References references
     String output_prefix
 
-    # this docker image was built using the commit hash f6cb51761861e57c43879aa262df5cf8e670cf7c (v2.0.1) from the VerifyBamID repo
-    # https://github.com/Griffan/VerifyBamID/commit/f6cb51761861e57c43879aa262df5cf8e670cf7c
-    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:1.0.1-f6cb51761861e57c43879aa262df5cf8e670cf7c-1692216226"
+
+    String docker = "us.gcr.io/broad-gotc-prod/verify-bam-id:f6cb51761861e57c43879aa262df5cf8e670cf7c-1606775309"
     Int disk_size_gb = ceil(if ceil((size(input_bam, "GB")) +
                             (size(references.ref_fasta, "GB") +
                             size(references.ref_fasta_index, "GB") +

diff --git a/website/docs/Pipelines/ATAC/README.md b/website/docs/Pipelines/ATAC/README.md
@@ -71,7 +71,7 @@ To see specific tool parameters, select the task WDL link in the table; then vie
 
 | Task name and WDL link | Tool | Software | Description | 
 | --- | --- | --- | ------------------------------------ | 
-| [FastqProcessing as SplitFastq](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/FastqProcessing.wdl) | fastqprocess | custom | Dynamically selects the correct barcode orientation, corrects cell barcodes and splits FASTQs into 30 GB FASTQs that are grouped by cell barcode with each read having the corrected (CB) and raw barcode (CR) in the read name. |
+| [FastqProcessing as SplitFastq](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/FastqProcessing.wdl) | fastqprocess | custom | Dynamically selects the correct barcode orientation, corrects cell barcodes and splits FASTQs into smaller FASTQs. The number of files output depends on either the bam_size parameter, which determines the size of the output FASTQs produced, or the num_output_files parameter, which determines the number of FASTQS that should be output. The smaller FASTQs are grouped by cell barcode with each read having the corrected (CB) and raw barcode (CR) in the read name. |
 | [TrimAdapters](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/multiome/atac.wdl) | Cutadapt v4.4 | cutadapt | Trims adaptor sequences. |
 | [BWAPairedEndAlignment](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/multiome/atac.wdl) | bwa-mem2 | mem | Aligns reads from each set of partitioned FASTQ files to the genome and outputs a BAM with ATAC barcodes in the CB:Z tag. |
 | [Merge.MergeSortBamFiles as MergeBam](https://github.com/broadinstitute/warp/blob/master/tasks/skylab/MergeSortBam.wdl) | MergeSamFiles | Picard | Merges each BAM into a final aligned BAM with corrected cell barcodes in the CB tag. |