call-sSV 3.0.0 release (#57)

* Update README.md

* Update pipeline version in nextflow.config

* fix README.md

* Update README.md

* Update CHANGELOG.md - Add 3.0.0 release section

Co-authored-by: Mootor <mmootor@ip-0A12523F.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>

CHANGELOG.md

@@ -8,6 +8,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [3.0.0] - 2022-07-25
 ### Added
 - Add F16.config to enable F16 node compatibility
 ### Changed

README.md

@@ -41,7 +41,7 @@ Pipelines should be run **WITH A SINGLE SAMPLE AT A TIME**. Otherwise resource a
 nextflow run path/to/main.nf -config path/to/sample-specific.config
 ```
 
-* For example, `path/to/main.nf` could be: `/hot/software/pipeline/pipeline-call-sSV/Nextflow/release/2.0.0/pipeline/call-sSV.nf`
+* For example, `path/to/main.nf` could be: `/hot/software/pipeline/pipeline-call-sSV/Nextflow/release/3.0.0/main.nf`
 * `path/to/sample-specific.config` is the path to where you saved your project-specific copy of [template.config](config/template.config) 
 
 To submit to UCLAHS-CDS's Azure cloud, use the submission script [here](https://github.com/uclahs-cds/tool-submit-nf) with the command below:
@@ -133,9 +133,9 @@ An example of the NextFlow Input Parameters Config file can be found [here](conf
 
 | Data Set | Run Configuration | Output Dir | Control Sample | Tumor Sample |  
 | ------ | ------ | ------- | ------ | ------- |
-| A-mini | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/A-mini-hg38.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/A-mini/call-sSV-2.0.0/S2.T-0/DELLY-1.0.3/output/ | /hot/resource/SMC-HET/normal/bams/A-mini/0/output/HG002.N-0.bam | /hot/resource/SMC-HET/tumours/A-mini/bams/0/output/S2.T-0.bam |
-| A-full | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/A-full-F72-hg19.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/A-full-F72/call-sSV-2.0.0/T5.T.sorted_py/DELLY-1.0.3/output/ | /hot/resource/SMC-HET/normal/bams/HG002.N.bam | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/input/T5.T.sorted_py.bam |
-| ILHNLNEV000001-T001-P01-F | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/ILHNLNEV000001-T001-P01-F-F32-hg38.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmoootor-upgrade-delly-0.9.1-to-1.0.3/ILHNLNEV000001-T001-P01-F-F32/call-sSV-2.0.0/ILHNLNEV000001-T001-P01-F_realigned_recalibrated_reheadered/DELLY-1.0.3/output/ | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000001-T001-P01-F/gSNP/2021-01-05_22.01.08/ILHNLNEV000001/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000001-N001-B01-F_realigned_recalibrated_reheadered.bam | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000001-T001-P01-F/gSNP/2021-01-05_22.01.08/ILHNLNEV000001/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000001-T001-P01-F_realigned_recalibrated_reheadered.bam |
+| A-mini | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/A-mini-hg38.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/A-mini/call-sSV-2.0.0/S2.T-0/DELLY-1.0.3/output/ | /hot/resource/SMC-HET/normal/bams/A-mini/0/output/HG002.N-0.bam | /hot/resource/SMC-HET/tumours/A-mini/bams/0/output/S2.T-0.bam |
+| A-full | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/A-full-F72-hg19.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/A-full-F72/call-sSV-2.0.0/T5.T.sorted_py/DELLY-1.0.3/output/ | /hot/resource/SMC-HET/normal/bams/HG002.N.bam | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/input/T5.T.sorted_py.bam |
+| ILHNLNEV000001-T001-P01-F | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/config/ILHNLNEV000001-T001-P01-F-F32-hg38.config | /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/3.0.0/mmoootor-upgrade-delly-0.9.1-to-1.0.3/ILHNLNEV000001-T001-P01-F-F32/call-sSV-2.0.0/ILHNLNEV000001-T001-P01-F_realigned_recalibrated_reheadered/DELLY-1.0.3/output/ | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000001-T001-P01-F/gSNP/2021-01-05_22.01.08/ILHNLNEV000001/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000001-N001-B01-F_realigned_recalibrated_reheadered.bam | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000001-T001-P01-F/gSNP/2021-01-05_22.01.08/ILHNLNEV000001/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000001-T001-P01-F_realigned_recalibrated_reheadered.bam |
 | ILHNLNEV000005-T002-L01-F | /hot/user/rhughwhite/ILHNLNEV/call-sSV/inputs_configs/2021-09-10/ILHNLNEV000005-T002-L01-F/nextflow.config | /hot/user/rhughwhite/ILHNLNEV/call-sSV/output/ILHNLNEV000005-T002-L01-F_testing/call-sSV-20210930-180357/ | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000005-T002-L01-F/gSNP/2021-01-08_17.01.47/ILHNLNEV000005/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000005-N001-B01-F_realigned_recalibrated_reheadered.bam | /hot/user/rhughwhite/ILHNLNEV/call-gSNP/output/2020-12-22/ILHNLNEV000005-T002-L01-F/gSNP/2021-01-08_17.01.47/ILHNLNEV000005/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000005-T002-L01-F_realigned_recalibrated_reheadered.bam |
 
 

nextflow.config

@@ -5,5 +5,5 @@ manifest {
     name = "call-sSV"
     author = "Yu Pan, Ghouse Mohammed, Mohammed Faizal Eeman Mootor"
     description = "A pipeline to call somatic SVs utilizing Delly"
-    version = "2.0.0"
+    version = "3.0.0"
     }