Merge pull request #603 from umccr/enhancement/add-ora-to-dragen-tran…

…scriptome-workflow

Added ora reference option to dragen transcriptome workflow

.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: bd7abab4ffef94a0ec7afd4e0589ccb5
+> md5sum: dabbfd88a4aaf041cba3496c9488bb84
 
 ### dragen-alignment v(4.0.3) documentation
 

.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: 6655c5981394561537d0dbdf48dc4525
+> md5sum: 97c5302d8c51ec0a7e1225447c1604b9
 
 ### dragen-alignment v(4.2.4) documentation
 

.github/catalogue/docs/tools/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: 7a4ade19434f610d11ab184870b25b55
+> md5sum: ddca7e05d6cce4a10451b639b447e444
 
 ### 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 0x7f22bc199e50>]`  
+**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7faa487f9e50>]`  
 **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 0x7f22bc3ccd60>]`  
+**Type:** `['File', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7faa48930d60>]`  
 **Docs:**  
 Specifies the BED file for base masking.
 

.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: 506167ae51734fd7f256da60db263f95
+> md5sum: 662b423443ae11af9ce3759977caf1bf
 
 ### dragen-germline v(4.0.3) documentation
 

.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: 2b5b45e49447cb8b282a053cdc071da1
+> md5sum: bb9225471e8137100924146d6aea109f
 
 ### dragen-germline v(4.2.4) documentation
 
@@ -395,6 +395,19 @@ Optional value, default set to /opt/instance-identity
 which is a path inside the dragen container
 
 
+### ora reference tar
+
+
+
+
+> ID: ora_reference_tar
+  
+**Optional:** `True`  
+**Type:** `File`  
+**Docs:**  
+Path to ORA ref data tarball
+
+
 ### output directory
 
 

.github/catalogue/docs/tools/dragen-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: 4f9305940dfb9e6e9a7b049cf0847834
+> md5sum: c4f06913c9d124ddc2fc194744822d32
 
 ### dragen-instrument-run-fastq-to-ora v(4.2.4) documentation
 

.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: 1f3a8b5e2791990e355cd5adc237d786
+> md5sum: 5acf07675dd681ea0de7705766db14e4
 
 ### 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 0x7fd556409910>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f4f23a41910>]`  
 **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). 

.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: 1d955db46be0e3926c6eabab31c1a817
+> md5sum: 89ea95ccb2da7b0add9f3bbe168f179f
 
 ### dragen-somatic v(4.2.4) documentation
 
@@ -519,6 +519,19 @@ Optional value, default set to /opt/instance-identity
 which is a path inside the dragen container
 
 
+### ora reference tar
+
+
+
+
+> ID: ora_reference_tar
+  
+**Optional:** `True`  
+**Type:** `File`  
+**Docs:**  
+Path to ORA ref data tarball
+
+
 ### output directory
 
 
@@ -1237,7 +1250,7 @@ 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 0x7f52584bdeb0>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7fb6d838f650>]`  
 **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).

.github/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: 90b2fda35b6efb41f2272f083d7a80e1
+> md5sum: 1665adc3fdb19069e1e302c70edc911b
 
 ### dragen-transcriptome v(4.0.3) documentation
 

.github/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: 38af34f5c16c605ad7bd06181934d9c8
+> md5sum: 7b27cf6088144ef7c4126429ad0f392b
 
 ### dragen-transcriptome v(4.2.4) documentation
 
@@ -202,6 +202,19 @@ Optional value, default set to /opt/instance-identity
 which is a path inside the dragen container
 
 
+### ora reference tar
+
+
+
+
+> ID: ora_reference_tar
+  
+**Optional:** `True`  
+**Type:** `File`  
+**Docs:**  
+Path to ORA ref data tarball
+
+
 ### output directory
 
 

.github/catalogue/docs/tools/multiqc/1.25.2/multiqc__1.25.2.md

@@ -0,0 +1,174 @@
+
+multiqc 1.25.2 tool
+===================
+
+## Table of Contents
+
+- [Overview](#multiqc-v1250-overview)  
+- [Links](#related-links)  
+- [Inputs](#multiqc-v1250-inputs)  
+- [Outputs](#multiqc-v1250-outputs)  
+- [ICA](#ica)  
+
+
+## multiqc v(1.25.0) Overview
+
+
+
+
+> ID: multiqc--1.25.0  
+> md5sum: 0886e525caeef6671f778e52463f244d
+
+### multiqc v(1.25.0) documentation
+
+Documentation for multiqc v1.25.0
+Use patch that includes https://github.com/ewels/MultiQC/pull/1969
+
+### Categories
+
+- qc  
+- visual  
+
+
+## Related Links
+
+- [CWL File Path](../../../../../../tools/multiqc/1.25.2/multiqc__1.25.2.cwl)  
+
+
+### Used By
+
+- [bclconvert-interop-qc 1.3.1--1.25.2](../../../workflows/bclconvert-interop-qc/1.3.1--1.25.2/bclconvert-interop-qc__1.3.1--1.25.2.md)  
+
+
+
+
+## multiqc v(1.25.0) Inputs
+
+### cl config
+
+
+
+
+> ID: cl_config
+  
+**Optional:** `True`  
+**Type:** `string`  
+**Docs:**  
+Override config from the cli
+
+
+### comment
+
+
+
+
+> ID: comment
+  
+**Optional:** `True`  
+**Type:** `string`  
+**Docs:**  
+Custom comment, will be printed at the top of the report.
+
+
+### config
+
+
+
+
+> ID: config
+  
+**Optional:** `True`  
+**Type:** `File`  
+**Docs:**  
+Configuration file for bclconvert
+
+
+### input directories
+
+
+
+
+> ID: input_directories
+  
+**Optional:** `False`  
+**Type:** `.[]`  
+**Docs:**  
+The list of directories to place in the analysis
+
+
+### output directory
+
+
+
+
+> ID: output_directory_name
+  
+**Optional:** `False`  
+**Type:** `string`  
+**Docs:**  
+The output directory
+
+
+### output filename
+
+
+
+
+> ID: output_filename
+  
+**Optional:** `False`  
+**Type:** `string`  
+**Docs:**  
+Report filename in html format.
+Defaults to 'multiqc-report.html"
+
+
+### title
+
+
+
+
+> ID: title
+  
+**Optional:** `False`  
+**Type:** `string`  
+**Docs:**  
+Report title.
+Printed as page header, used for filename if not otherwise specified.
+
+
+
+
+## multiqc v(1.25.0) Outputs
+
+### output directory
+
+
+
+
+> ID: multiqc--1.25.0/output_directory  
+
+
+**Optional:** `False`  
+**Output Type:** `Directory`  
+**Docs:**  
+Directory that contains all multiqc analysis data
+
+
+
+### output file
+
+
+
+
+> ID: multiqc--1.25.0/output_file  
+
+
+**Optional:** `False`  
+**Output Type:** `File`  
+**Docs:**  
+Output html file
+
+
+
+

.github/catalogue/docs/workflows/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: 53ddc08bf654bf03bffc7edb4a3ccdf6
+> md5sum: dfad0c0195611d1ff0ca6a255955fc00
 
 ### bclconvert-interop-qc v(1.3.1--1.21) documentation