nf-core · tanyasarkjain · Mar 6, 2025 · Feb 12, 2025 · Feb 12, 2025 · Feb 12, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0.0 - Goldfish [01/31/2025]
-
-Initial release of nf-core/pacvar, created with the [nf-core](https://nf-co.re/) template.
+## v1.0.1 - Sardine [02/26/2025]
-## v1.0.1 - Sardine [02/26/2025]
+## v1.0.1 - Sardine [2025-03-06]
-## v1.0.1 - Sardine [02/26/2025]
+## v1.0.1 - Sardine [2025-03-06]
 
 ### `Added`
 
 ### `Fixed`
 
+- [#19](https://github.com/nf-core/pacvar/pull/19) Changed files produced downstream from PBSV to have an output file name containing 'sv' to indicate origin of the files, as with those files downstream from GATK4 and Deepvariant have 'snv' in output file name (@tanyasarkjain)
+- [#21](https://github.com/nf-core/pacvar/pull/21) Tweaks to the channels passed into HiPhase - specifically ensure that the inputted VCF and BAM channel are ordered in the same way (according to their shared meta). (@tanyasarkjain)
+
 ### `Dependencies`
 
 ### `Deprecated`
+
+## v1.0.0 - Goldfish [01/31/2025]
-## v1.0.0 - Goldfish [01/31/2025]
+## v1.0.0 - Goldfish [2025-01-31]
-## v1.0.0 - Goldfish [01/31/2025]
+## v1.0.0 - Goldfish [2025-01-31]
+
+Initial release of nf-core/pacvar, created with the [nf-core](https://nf-co.re/) template.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pacvar/releases/tag/1.0.0" target="_blank">nf-core/pacvar</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pacvar/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pacvar/releases/tag/1.0.1"
+  target="_blank">nf-core/pacvar</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/pacvar/1.0.1/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pacvar-methods-description":
     order: -1000

diff --git a/conf/modules.config b/conf/modules.config
@@ -31,7 +31,7 @@ process {
     }
 
     withName: 'PBSV_CALL' {
-        ext.prefix = { "${meta.id}.pbsv" }
+        ext.prefix = { "${meta.id}.sv" }
     }
 
     withName: 'LIMA' {
@@ -54,5 +54,28 @@ process {
         ext.prefix = {"${meta.id}.trgt.sorted"}
     }
 
+    withName: 'TABIX_BGZIP' {
+        ext.prefix = {"${meta.id}.sv"}
+    }
+
+    withName: '.*:BAM_SV_VARIANT_CALLING:BCFTOOLS_INDEX' {
+        ext.prefix = { "${meta.id}.sv" }
+    }
 
+    withName: 'HIPHASE_SV' {
+        ext.prefix = {"${meta.id}.sv"}
+    }
+
+    withName: 'HIPHASE_SNP' {
+        ext.prefix = {"${meta.id}.snv"}
+    }
+
+
+    withName: 'GATK4_HAPLOTYPECALLER' {
+        ext.prefix = {"${meta.id}.snv"}
+    }
+
+    withName: 'DEEPVARIANT' {
+        ext.prefix = {"${meta.id}.snv"}
+    }
 }
diff --git a/conf/test_wgs_gatk.config b/conf/test_wgs_gatk.config
@@ -34,5 +34,4 @@ params {
     snv_caller                  = 'gatk4'
     intervals                   = params.pipelines_testdata_base_path + 'pacbio_data/c9orf72-short.bed'
     workflow                    = 'wgs'
-    skip_phase                  = true
 }
diff --git a/docs/output.md b/docs/output.md
@@ -78,8 +78,8 @@ Note:
 <summary>Output files</summary>
 
 - `gatk4/`
-  - `<basename>.vcf.gz`: VCF of the SNV
-  - `<basename>.vcf.gz.tbi`: Associated indexes for the VCF files
+  - `<basename>.snv.vcf.gz`: VCF of the SNV
+  - `<basename>.snv.vcf.gz.tbi`: Associated indexes for the VCF files
 
 </details>
 
@@ -91,7 +91,7 @@ Note:
 <summary>Output files</summary>
 
 - `pbsv/`
-  - `<basename>.pbsv.vcf`: VCF of SV
+  - `<basename>.sv.vcf`: VCF of SV
   - `<basename>.svsig.gz`: File containing signatures of structural variants
 
 </details>
@@ -104,9 +104,12 @@ Note:
 <summary>Output files</summary>
 
 - `hiphase/`
-  - `<basename>.phased.bam`: Haplotagged BAM
-  - `<basename>.phased.vcf`: The phased Variant File
-  - `<basename>.phased.vcf`: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase.
+  - `<basename>.snv.phased.bam`: Haplotagged BAM - outputted from phasing based on SNV
+  - `<basename>.sv.phased.bam`: Haplotagged BAM - outputted from phasing based on SV
+  - `<basename>.snv.phased.vcf`: The phased Variant File (SNV) (Zipped)
+  - `<basename>.sv.phased.vcf`: The phased Variant File (SV) (Zipped)
+  - `<basename>.snv.stats.csv`: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase (SNV)
+  - `<basename>.sv.stats.csv`: This CSV/TSV file contains information about the the phase blocks that were output by HiPhase (SV)
 
 </details>
 
@@ -118,7 +121,7 @@ Note:
 <summary>Output files</summary>
 
 - `tabix/`
-  - `<basename>.vcf.gz`: Zipped PBSV VCF files
+  - `<basename>.sv.vcf.gz`: Zipped PBSV VCF files
 
 </details>
 
@@ -130,7 +133,7 @@ Note:
 <summary>Output files</summary>
 
 - `BCFTOOLS/`
-  - `<basename>.vcf.gz.csi`: Index of PBSV VCF files
+  - `<basename>.sv.vcf.gz.csi`: Index of PBSV VCF files
 
 </details>
 
@@ -142,8 +145,8 @@ Note:
 <summary>Output files</summary>
 
 - `deepvariant/`
-  - `<basename>.vcf.gz`: Zipped VCF file
-  - `<basename>.vcf.gz.tbi`: Associated index to zipped VCF file
+  - `<basename>.snv.vcf.gz`: Zipped VCF file
+  - `<basename>.snv.vcf.gz.tbi`: Associated index to zipped VCF file
 
 </details>
 

diff --git a/modules/nf-core/pbmm2/align/main.nf b/modules/nf-core/pbmm2/align/main.nf
diff --git a/modules/nf-core/pbmm2/align/pbmm2-align.diff b/modules/nf-core/pbmm2/align/pbmm2-align.diff
diff --git a/nextflow.config b/nextflow.config
@@ -274,7 +274,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0.0'
+    version         = '1.0.1'
     doi             = '10.5281/zenodo.14813048'
 }