Merge branch 'release_191' into 'dev'

Tag version and minor fix to docs See merge request epi2melabs/workflows/wf-human-variation!178
epi2me-labs · Dec 6, 2023 · dfde912 · dfde912
2 parents 61b24e3 + e003001
commit dfde912
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
-## [unreleased]
+## [v1.9.1]
 ### Changed
 - ClinVar annotation of SVs has been temporarily removed due to not being correctly incorporated. SnpEff annotations are still produced as part of the final SV VCF.
 - New documentation

diff --git a/README.md b/README.md
@@ -219,10 +219,10 @@ Outputs files may be aggregated including information for all samples or provide
 | Copy number variants VCF | {{ alias }}.wf_cnv.vcf.gz | VCF file with the CNV for the sample. | per-sample |
 | Modified bases BEDMethyl | {{ alias }}.wf_mods.bedmethyl.gz | BED file with the aggregated modification counts for the sample. | per-sample |
 | Short tandem repeat VCF | {{ alias }}.wf_str.vcf.gz | VCF file with the STR sites for the sample. | per-sample |
-| Alignment file | {{ alias }}.{{ format }} | BAM or CRAM file with the aligned reads for the sample, generated when the input file is unaligned. | per-sample |
-| Alignment file index | {{ alias }}.{{ format }}.{{ index_format }} | The index of the resulting BAM or CRAM file with the reads for the sample, generated when the input file is unaligned. | per-sample |
-| Haplotagged alignment file | {{ alias }}.haplotagged.{{ format }} | BAM or CRAM file with the haplotagged reads for the sample. | per-sample |
-| Haplotagged alignment file index | {{ alias }}.haplotagged.{{ format }}.{{ index_format }} | The index of the resulting BAM or CRAM file with the haplotagged reads for the sample. | per-sample |
+| Alignment file | {{ alias }}.cram | CRAM or BAM file with the aligned reads for the sample, generated when the input file is unaligned. | per-sample |
+| Alignment file index | {{ alias }}.cram.crai | The index of the resulting CRAM or BAM file with the reads for the sample, generated when the input file is unaligned. | per-sample |
+| Haplotagged alignment file | {{ alias }}.haplotagged.cram | CRAM or BAM file with the haplotagged reads for the sample. | per-sample |
+| Haplotagged alignment file index | {{ alias }}.haplotagged.cram.crai | The index of the resulting CRAM or BAM file with the haplotagged reads for the sample. | per-sample |
 
 
 

diff --git a/docs/07_outputs.md b/docs/07_outputs.md
@@ -13,7 +13,7 @@ Outputs files may be aggregated including information for all samples or provide
 | Copy number variants VCF | {{ alias }}.wf_cnv.vcf.gz | VCF file with the CNV for the sample. | per-sample |
 | Modified bases BEDMethyl | {{ alias }}.wf_mods.bedmethyl.gz | BED file with the aggregated modification counts for the sample. | per-sample |
 | Short tandem repeat VCF | {{ alias }}.wf_str.vcf.gz | VCF file with the STR sites for the sample. | per-sample |
-| Alignment file | {{ alias }}.{{ format }} | BAM or CRAM file with the aligned reads for the sample, generated when the input file is unaligned. | per-sample |
-| Alignment file index | {{ alias }}.{{ format }}.{{ index_format }} | The index of the resulting BAM or CRAM file with the reads for the sample, generated when the input file is unaligned. | per-sample |
-| Haplotagged alignment file | {{ alias }}.haplotagged.{{ format }} | BAM or CRAM file with the haplotagged reads for the sample. | per-sample |
-| Haplotagged alignment file index | {{ alias }}.haplotagged.{{ format }}.{{ index_format }} | The index of the resulting BAM or CRAM file with the haplotagged reads for the sample. | per-sample |
+| Alignment file | {{ alias }}.cram | CRAM or BAM file with the aligned reads for the sample, generated when the input file is unaligned. | per-sample |
+| Alignment file index | {{ alias }}.cram.crai | The index of the resulting CRAM or BAM file with the reads for the sample, generated when the input file is unaligned. | per-sample |
+| Haplotagged alignment file | {{ alias }}.haplotagged.cram | CRAM or BAM file with the haplotagged reads for the sample. | per-sample |
+| Haplotagged alignment file index | {{ alias }}.haplotagged.cram.crai | The index of the resulting CRAM or BAM file with the haplotagged reads for the sample. | per-sample |
diff --git a/nextflow.config b/nextflow.config
@@ -161,7 +161,7 @@ manifest {
     description     = 'Basecalling, SNV calling, SV calling, modified base calling, CNV calling, and STR genotyping of human samples.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = '1.9.0'
+    version         = '1.9.1'
 }
 
 epi2melabs {

diff --git a/output_definition.json b/output_definition.json
@@ -89,33 +89,33 @@
       "type": "per-sample"
     },
     "alignment": {
-      "filepath": "{{ alias }}.{{ format }}",
+      "filepath": "{{ alias }}.cram",
       "title": "Alignment file",
-      "description": "BAM or CRAM file with the aligned reads for the sample, generated when the input file is unaligned.",
+      "description": "CRAM or BAM file with the aligned reads for the sample, generated when the input file is unaligned.",
       "mime-type": "application/gzip",
       "optional": true,
       "type": "per-sample"
     },    
     "alignment-index": {
-      "filepath": "{{ alias }}.{{ format }}.{{ index_format }}",
+      "filepath": "{{ alias }}.cram.crai",
       "title": "Alignment file index",
-      "description": "The index of the resulting BAM or CRAM file with the reads for the sample, generated when the input file is unaligned.",
+      "description": "The index of the resulting CRAM or BAM file with the reads for the sample, generated when the input file is unaligned.",
       "mime-type": "application/octet-stream",
       "optional": true,
       "type": "per-sample"
     },
     "haplotagged-alignment": {
-      "filepath": "{{ alias }}.haplotagged.{{ format }}",
+      "filepath": "{{ alias }}.haplotagged.cram",
       "title": "Haplotagged alignment file",
-      "description": "BAM or CRAM file with the haplotagged reads for the sample.",
+      "description": "CRAM or BAM file with the haplotagged reads for the sample.",
       "mime-type": "application/gzip",
       "optional": true,
       "type": "per-sample"
     },    
     "haplotagged-alignment-index": {
-      "filepath": "{{ alias }}.haplotagged.{{ format }}.{{ index_format }}",
+      "filepath": "{{ alias }}.haplotagged.cram.crai",
       "title": "Haplotagged alignment file index",
-      "description": "The index of the resulting BAM or CRAM file with the haplotagged reads for the sample.",
+      "description": "The index of the resulting CRAM or BAM file with the haplotagged reads for the sample.",
       "mime-type": "application/octet-stream",
       "optional": true,
       "type": "per-sample"