Pull request #9: [SEQL-663] directory fixMerge in BCAT/pmc-scripts from feature/SEQL-664-cnspectorx-tcrp_3-script-changes to dev
* commit 'a1d4fbd35fceb90242b741e87e72852f53b1d0e5':
[SEQL-663] directory fix
Pull request #8: Feature/SEQL-664 cnspectorx tcrp 3 script changesMerge in BCAT/pmc-scripts from feature/SEQL-664-cnspectorx-tcrp_3-script-changes to dev
* commit '76af5a3a1685cb9d751af1c6f9e7be215e46b275':
[SEQL-664] receive panel parameter from cnx step2 and use it in place of hardcoded Pathology_hyb_TCRP_1
[SEQL-664] update static reference script to take panel parameter
Pull request #7: [CLP-145] Inferred_sex column for TCRP panelMerge in BCAT/pmc-scripts from inferred_sex-TCRP to dev
* commit 'bc3b3759079c4249e72a2e0adb4655ee5bba0ebe':
[CLP-145] Inferred_sex column for TCRP panel
Pull request #6: [SEQL-657] point to new transcript id fileMerge in BCAT/pmc-scripts from feature/SEQL-657-point-seqcnv-table-script-to-new-txid-file to dev
* commit 'e8248379da8bda4173aba476877cc16cede266d5':
[SEQL-657] point to new transcript id file
Pull request #3: [CLP-626] add TWIST multiqc yaml config file, pathos query python script, and modify run_HYSYS to add highest concordance table creationMerge in BCAT/pmc-scripts from ~TIMOTHEE.FROUTE/pmc-scripts-twist-multiqc:twist_multiqc to dev
* commit 'bc0c387e1cb0e10f19a08f5aa19faaf0e54df5b0':
add IDS_NOT_CHECKED tag if patient IDs can't be retrieved from pathos
add module version
[CLP-626] add TWIST multiqc yaml config file, pathos query python script, and modify run_HYSYS to add highest concordance table
Pull request #2: Feature/SEQL-602 add gaffa related workflows to janisMerge in BCAT/pmc-scripts from feature/SEQL-602-add-gaffa-related-workflows-to-janis to master
* commit '1ddf0c7e7ac70dba5353bd85c8562286b1e0eb5b':
[SEQL-602] update script to take gaffa reference path as argument
[SEQL-602] change paths to account for <sample>/CNV structure
[SEQL-602] script for creating CNSpectorX static reference folder
[SEQL-602] adding GenerateGaffaDCF and gaffa_p...
Pull request #1: pmc-scripts 2.16Merge in BCAT/pmc-scripts from dev to master
* commit 'd0fff98381a99a680e486969daf98b1376188aca':
[SEQL-584] [Clinical Pipelines] Minor fix to MegaFusion tsv to vcf conversion
[CLP-582] Replaced 'http://bioinf-ensembl.petermac.org.au' with 'https://bioinf-pathos.petermac.org.au' in links in subpanels table so that it works now that PathOS UAT & PROD are on 'https' server.
[CLP-581] Added...
[CLP-582] Replaced 'http://bioinf-ensembl.petermac.org.au' with 'https://bioinf-pathos.petermac.org.au' in links in subpanels table so that it works now that PathOS UAT & PROD are on 'https' server.
