Merge pull request #573 from umccr/fix/split-cnv-by-germline-and-somatic

umccr · Nov 7, 2024 · 2d000a9 · 2d000a9
2 parents 72d3a0e + 17b6609
commit 2d000a9
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diff --git a/.github/catalogue/docs/tools/dragen-alignment/4.0.3/dragen-alignment__4.0.3.md b/.github/catalogue/docs/tools/dragen-alignment/4.0.3/dragen-alignment__4.0.3.md
@@ -17,7 +17,7 @@ dragen-alignment 4.0.3 tool
 
 
 > ID: dragen-alignment--4.0.3  
-> md5sum: 06f52a5f9a19df120c173dd7b2aad02d
+> md5sum: bd7abab4ffef94a0ec7afd4e0589ccb5
 
 ### dragen-alignment v(4.0.3) documentation
 

diff --git a/.github/catalogue/docs/tools/dragen-alignment/4.2.4/dragen-alignment__4.2.4.md b/.github/catalogue/docs/tools/dragen-alignment/4.2.4/dragen-alignment__4.2.4.md
@@ -17,7 +17,7 @@ dragen-alignment 4.2.4 tool
 
 
 > ID: dragen-alignment--4.2.4  
-> md5sum: 2a9a2eec633f9c2ea3174a23e56e9f21
+> md5sum: 6655c5981394561537d0dbdf48dc4525
 
 ### dragen-alignment v(4.2.4) documentation
 

diff --git a/...s/dragen-build-reference-tarball/4.2.4/dragen-build-reference-tarball__4.2.4.md b/...s/dragen-build-reference-tarball/4.2.4/dragen-build-reference-tarball__4.2.4.md
@@ -17,7 +17,7 @@ dragen-build-reference-tarball 4.2.4 tool
 
 
 > ID: dragen-build-reference-tarball--4.2.4  
-> md5sum: dceef6b98beb9e0840a8f5ec9b2e1eb4
+> md5sum: 7a4ade19434f610d11ab184870b25b55
 
 ### dragen-build-reference-tarball v(4.2.4) documentation
 
@@ -77,7 +77,7 @@ To disable this requirement, set the --ht-alt-aware-validate option to false.
 > ID: ht_alt_liftover
   
 **Optional:** `True`  
-**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f4955d9ee40>]`  
+**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f22bc199e50>]`  
 **Docs:**  
 The --ht-alt-liftover option specifies the path to the liftover file to build an ALT-aware hash table.
 This option is required when building from a reference with ALT contigs.
@@ -204,7 +204,7 @@ The default is /opt/edico/liftover/hs_decoys.fa.
 > ID: ht_mask_bed
   
 **Optional:** `True`  
-**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f4955d9f980>]`  
+**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f22bc3ccd60>]`  
 **Docs:**  
 Specifies the BED file for base masking.
 

diff --git a/.github/catalogue/docs/tools/dragen-germline/4.0.3/dragen-germline__4.0.3.md b/.github/catalogue/docs/tools/dragen-germline/4.0.3/dragen-germline__4.0.3.md
@@ -17,7 +17,7 @@ dragen-germline 4.0.3 tool
 
 
 > ID: dragen-germline--4.0.3  
-> md5sum: 78fc17bcadd751c67e772c422cf53487
+> md5sum: 506167ae51734fd7f256da60db263f95
 
 ### dragen-germline v(4.0.3) documentation
 

diff --git a/.github/catalogue/docs/tools/dragen-germline/4.2.4/dragen-germline__4.2.4.md b/.github/catalogue/docs/tools/dragen-germline/4.2.4/dragen-germline__4.2.4.md
@@ -17,7 +17,7 @@ dragen-germline 4.2.4 tool
 
 
 > ID: dragen-germline--4.2.4  
-> md5sum: e52da4f95f01382810a29afae0326d1c
+> md5sum: 2b5b45e49447cb8b282a053cdc071da1
 
 ### dragen-germline v(4.2.4) documentation
 

diff --git a/...-instrument-run-fastq-to-ora/4.2.4/dragen-instrument-run-fastq-to-ora__4.2.4.md b/...-instrument-run-fastq-to-ora/4.2.4/dragen-instrument-run-fastq-to-ora__4.2.4.md
@@ -17,7 +17,7 @@ dragen-instrument-run-fastq-to-ora 4.2.4 tool
 
 
 > ID: dragen-instrument-run-fastq-to-ora--4.2.4  
-> md5sum: 446649b855aac94789ac8142821e07bf
+> md5sum: 4f9305940dfb9e6e9a7b049cf0847834
 
 ### dragen-instrument-run-fastq-to-ora v(4.2.4) documentation
 

diff --git a/.github/catalogue/docs/tools/dragen-somatic/4.0.3/dragen-somatic__4.0.3.md b/.github/catalogue/docs/tools/dragen-somatic/4.0.3/dragen-somatic__4.0.3.md
@@ -17,7 +17,7 @@ dragen-somatic 4.0.3 tool
 
 
 > ID: dragen-somatic--4.0.3  
-> md5sum: 10df7471fbd55e1774f47c8465f12b72
+> md5sum: 1f3a8b5e2791990e355cd5adc237d786
 
 ### dragen-somatic v(4.0.3) documentation
 
@@ -1113,7 +1113,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f958a2abf50>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7fd556409910>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter. 
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads). 

diff --git a/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md b/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md
@@ -17,7 +17,7 @@ dragen-somatic 4.2.4 tool
 
 
 > ID: dragen-somatic--4.2.4  
-> md5sum: 013f7568205a09ec35db6c3e000e8966
+> md5sum: 1d955db46be0e3926c6eabab31c1a817
 
 ### dragen-somatic v(4.2.4) documentation
 
@@ -1237,7 +1237,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f4c22d70e60>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f52584bdeb0>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).

diff --git a/.../catalogue/docs/tools/dragen-transcriptome/4.0.3/dragen-transcriptome__4.0.3.md b/.../catalogue/docs/tools/dragen-transcriptome/4.0.3/dragen-transcriptome__4.0.3.md
@@ -17,7 +17,7 @@ dragen-transcriptome 4.0.3 tool
 
 
 > ID: dragen-transcriptome--4.0.3  
-> md5sum: ecda91d92d46dcae1a39f7a412af47b0
+> md5sum: 90b2fda35b6efb41f2272f083d7a80e1
 
 ### dragen-transcriptome v(4.0.3) documentation
 

diff --git a/.../catalogue/docs/tools/dragen-transcriptome/4.2.4/dragen-transcriptome__4.2.4.md b/.../catalogue/docs/tools/dragen-transcriptome/4.2.4/dragen-transcriptome__4.2.4.md
@@ -17,7 +17,7 @@ dragen-transcriptome 4.2.4 tool
 
 
 > ID: dragen-transcriptome--4.2.4  
-> md5sum: 5880061f6662ed9608f2ec996b3e882a
+> md5sum: 38af34f5c16c605ad7bd06181934d9c8
 
 ### dragen-transcriptome v(4.2.4) documentation
 

diff --git a/...rkflows/bclconvert-interop-qc/1.3.1--1.21/bclconvert-interop-qc__1.3.1--1.21.md b/...rkflows/bclconvert-interop-qc/1.3.1--1.21/bclconvert-interop-qc__1.3.1--1.21.md
@@ -19,7 +19,7 @@ bclconvert-interop-qc 1.3.1--1.21 workflow
 
 
 > ID: bclconvert-interop-qc--1.3.1--1.21  
-> md5sum: ac758f18a4438440d8c1cae45eb5ffb1
+> md5sum: 53ddc08bf654bf03bffc7edb4a3ccdf6
 
 ### bclconvert-interop-qc v(1.3.1--1.21) documentation
 

diff --git a/.../catalogue/docs/workflows/bclconvert-scatter/4.0.3/bclconvert-scatter__4.0.3.md b/.../catalogue/docs/workflows/bclconvert-scatter/4.0.3/bclconvert-scatter__4.0.3.md
@@ -19,7 +19,7 @@ bclconvert-scatter 4.0.3 workflow
 
 
 > ID: bclconvert-scatter--4.0.3  
-> md5sum: 8c7cc67af160644d95504a546c0da14f
+> md5sum: 8a12e723bb4c3377bbaea22f5ec0cbc3
 
 ### bclconvert-scatter v(4.0.3) documentation
 

diff --git a/...rkflows/bclconvert-with-qc-pipeline/4.0.3/bclconvert-with-qc-pipeline__4.0.3.md b/...rkflows/bclconvert-with-qc-pipeline/4.0.3/bclconvert-with-qc-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ bclconvert-with-qc-pipeline 4.0.3 workflow
 
 
 > ID: bclconvert-with-qc-pipeline--4.0.3  
-> md5sum: 4bde2320aabf1be49817fdba4335e0ac
+> md5sum: 50807dec71c19051055c01729a358d75
 
 ### bclconvert-with-qc-pipeline v(4.0.3) documentation
 

diff --git a/...s/workflows/dragen-alignment-pipeline/4.0.3/dragen-alignment-pipeline__4.0.3.md b/...s/workflows/dragen-alignment-pipeline/4.0.3/dragen-alignment-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ dragen-alignment-pipeline 4.0.3 workflow
 
 
 > ID: dragen-alignment-pipeline--4.0.3  
-> md5sum: 9b2dae82000d09aefa240c759bbaec76
+> md5sum: 5aa4890ae0a27d6d6af0b6de85376aed
 
 ### dragen-alignment-pipeline v(4.0.3) documentation
 

diff --git a/...s/workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.md b/...s/workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-alignment-pipeline 4.2.4 workflow
 
 
 > ID: dragen-alignment-pipeline--4.2.4  
-> md5sum: 54e2dd90864bb85f334af92d4e255da1
+> md5sum: 52e52401333e436b158af011a8a8f424
 
 ### dragen-alignment-pipeline v(4.2.4) documentation
 
@@ -967,7 +967,7 @@ The dragen multiQC output
 
 
 **workflow name:** dragen-alignment-pipeline_prod-wf  
-**wfl version name:** 4.2.4--1c67c7b  
+**wfl version name:** 4.2.4--89be8f2