diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 71be093e..ec7f860f 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.5
+current_version = 1.0.0
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?
 serialize = 
diff --git a/.github/workflows/conda_docker_pkgdown.yml b/.github/workflows/conda_docker_pkgdown.yml
index 4b2820cb..3d96beb9 100644
--- a/.github/workflows/conda_docker_pkgdown.yml
+++ b/.github/workflows/conda_docker_pkgdown.yml
@@ -9,7 +9,7 @@ env:
   recipe_path: deploy/conda/recipe
   env_yaml_path: deploy/conda/env/yaml
   env_lock_path: deploy/conda/env/lock
-  VERSION: '0.6.5' # versioned by bump2version
+  VERSION: '1.0.0' # versioned by bump2version
 
 jobs:
   condarise-dockerise-document:
diff --git a/DESCRIPTION b/DESCRIPTION
index 0af461a9..6153c3be 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RNAsum
 Title: A Robust Tool for Performing Transcriptome Profiling on Cancer Data
-Version: 0.6.5
+Version: 1.0.0
 Authors@R: 
     c(person(given = "Sehrish",
              family = "Kanwal",
diff --git a/README.Rmd b/README.Rmd
index f2d460ce..8649f5e7 100755
--- a/README.Rmd
+++ b/README.Rmd
@@ -211,9 +211,8 @@ export PATH="${rnasum_cli}:${PATH}"
 rnasum_cli=$(Rscript -e 'x = system.file("cli", package = "RNAsum"); cat(x, "\n")' | xargs)
 export PATH="${rnasum_cli}:${PATH}"
 
-# TODO: implement version flag
 echo "$ rnasum.R --version"
-echo "rnasum.R x.x.x"
+rnasum.R --version
 echo ""
 echo "$ rnasum.R --help"
 rnasum.R --help
diff --git a/README.md b/README.md
index 4a65f621..922e9de0 100755
--- a/README.md
+++ b/README.md
@@ -215,106 +215,115 @@ export PATH="${rnasum_cli}:${PATH}"
 ```
 
     $ rnasum.R --version
-    rnasum.R x.x.x
+    1.0.0 
 
     $ rnasum.R --help
     Usage
     =====
      
-    /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RNAsum/cli/rnasum.R [options]
+    /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RNAsum/cli/rnasum.R [options]
 
 
     Options
     =======
+    --arriba_dir=ARRIBA_DIR
+            Directory path to Arriba results containing fusions.pdf and fusions.tsv.
+
     --arriba_pdf=ARRIBA_PDF
-            File path of Arriba PDF output
+            File path of Arriba PDF output.
 
     --arriba_tsv=ARRIBA_TSV
-            File path of Arriba TSV output
+            File path of Arriba TSV output.
 
-    --batch_rm=BATCH_RM
-            Remove batch-associated effects between datasets? [def: TRUE]
+    --batch_rm
+            Remove batch-associated effects between datasets.
 
     --cn_gain=CN_GAIN
-            CN threshold value to classify genes within gained regions [def: 95]
+            CN threshold value to classify genes within gained regions. [def: 95]
 
     --cn_loss=CN_LOSS
-            CN threshold value to classify genes within lost regions [def: 5]
+            CN threshold value to classify genes within lost regions. [def: 5]
 
     --dataset=DATASET
-            Dataset to be used as external reference cohort [def: PANCAN]
+            Dataset to be used as external reference cohort. [def: PANCAN]
 
-    --dataset_name_incl=DATASET_NAME_INCL
-            Include dataset in report name? [def: FALSE]
+    --dataset_name_incl
+            Include dataset in report name.
 
     --dragen_fusions=DRAGEN_FUSIONS
-            File path to DRAGEN RNA-seq 'fusion_candidates.final' output
+            File path to DRAGEN RNA-seq 'fusion_candidates.final' output.
+
+    --dragen_mapping_metrics=DRAGEN_MAPPING_METRICS
+            File path to DRAGEN RNA-seq 'mapping_metrics.csv' output.
 
-    --drugs=DRUGS
-            Include drug matching section in report? [def: FALSE]
+    --dragen_wts_dir=DRAGEN_WTS_DIR
+            Directory path to DRAGEN RNA-seq results.
 
-    --filter=FILTER
-            Filter out low expressed genes? [def: TRUE]
+    --drugs
+            Include drug matching section in report.
 
-    --hide_code_btn=HIDE_CODE_BTN
-            Hide "Code" button above code chunks in report? [def: TRUE]
+    --filter
+            Filter out low expressed genes.
 
-    --immunogram=IMMUNOGRAM
-            Include immunogram in report? [def: FALSE]
+    --immunogram
+            Include immunogram in report.
 
-    --log=LOG
-            Log2 transform data before normalisation? [def: TRUE]
+    --log
+            Log2 transform data before normalisation.
 
     --manta_tsv=MANTA_TSV
-            File path to umccrise 'manta.tsv' output
+            File path to umccrise 'manta.tsv' output.
 
     --norm=NORM
-            Normalisation method
+            Normalisation method.
 
-    --pcgr_splice_vars=PCGR_SPLICE_VARS
-            Include non-coding splice region variants reported in PCGR? [def: TRUE]
+    --pcgr_splice_vars
+            Include non-coding splice region variants reported in PCGR.
 
     --pcgr_tier=PCGR_TIER
-            Tier threshold for reporting variants reported in PCGR [def: 4]
+            Tier threshold for reporting variants reported in PCGR. [def: 4]
 
     --pcgr_tiers_tsv=PCGR_TIERS_TSV
-            File path to PCGR 'snvs_indels.tiers.tsv' output
+            File path to PCGR 'snvs_indels.tiers.tsv' output.
 
     --project=PROJECT
-            Project name
+            Project name, used for annotation purposes only.
 
     --purple_gene_tsv=PURPLE_GENE_TSV
-            File path to PURPLE 'purple.cnv.gene.tsv' output
+            File path to PURPLE 'purple.cnv.gene.tsv' output.
 
     --report_dir=REPORT_DIR
-            Directory path to output report
+            Directory path to output report.
 
     --salmon=SALMON
-            File path to salmon 'quant.sf' output
+            File path to salmon 'quant.genes.sf' output.
 
     --sample_name=SAMPLE_NAME
-            Sample name to be presented in report
+            Sample name to be presented in report.
 
     --sample_source=SAMPLE_SOURCE
-            Type of investigated sample [def: -]
+            Type of investigated sample. [def: -]
 
-    --save_tables=SAVE_TABLES
-            Save interactive summary tables as HTML? [def: TRUE]
+    --save_tables
+            Save interactive summary tables as HTML.
 
     --scaling=SCALING
-            Scaling for z-score transformation (gene-wise or group-wise) [def: gene-wise]
+            Scaling for z-score transformation (gene-wise or group-wise). [def: gene-wise]
 
     --subject_id=SUBJECT_ID
-            Subject ID
+            Subject ID.
 
     --top_genes=TOP_GENES
-            Number of top ranked genes to be presented in report
+            Number of top ranked genes to be presented in report.
 
     --transform=TRANSFORM
-            Transformation method to be used when converting read counts [def: CPM]
+            Transformation method to be used when converting read counts. [def: CPM]
 
     --umccrise=UMCCRISE
-            Directory path of the corresponding WGS-related data
+            Directory path of the corresponding WGS-related umccrise data.
+
+    --version, -v
+            Print RNAsum version and exit.
 
     --help, -h
             Show this help message and exit
@@ -471,3 +480,7 @@ prioritisation and visualisation is available
 
 The `results` folder contains intermediate files, including plots and
 tables that are presented in the HTML report.
+
+#### Code of Conduct
+
+The code of conduct can be accessed [here](./CODE_OF_CONDUCT.md).
diff --git a/deploy/conda/env/lock/rnasum-linux-64.lock b/deploy/conda/env/lock/rnasum-linux-64.lock
index 3aaaaf45..c6f3d0cf 100644
--- a/deploy/conda/env/lock/rnasum-linux-64.lock
+++ b/deploy/conda/env/lock/rnasum-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: ab9c8dc56760277f4f16a0fe91cab4879b8230efb2d811f7ee8ae136ed65891a
+# input_hash: 39aa837f70d47f1ee3519430ae37e5481be3c9e177b681775965a55ce166c4d9
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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@@ -8,41 +8,43 @@ https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca05
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-https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
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-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-ha9c7c90_105.conda#3bc29a967fee57e193ce51f51c598bca
-https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-ha9c7c90_105.conda#66383205c2e1bdf013df52fa9e3e6763
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-hceb6213_107.conda#2cc37ba482c6321237ce72329e1aaea2
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hceb6213_107.conda#2b409e9645fb3d69115d04496d1219cc
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
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-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
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-https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-hf600244_0.conda#33084421a8c0af6aef1b439707f7662a
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha885e6a_0.conda#800a4c872b5bc06fa83888d112fe6c4f
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+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
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-https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37
+https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033
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+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede
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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-hca663fb_7.conda#c0bd771f09a326fdcd95a60b617795bf
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-https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-13.2.0-h7e041cc_5.conda#3f686300a92604d1bdff9a29dd4a6639
+https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-13.2.0-h6ddb7a1_7.conda#ecba88d2296bf40186a9dc65bdf7b621
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-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
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-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda#fcea371545eda051b6deafb24889fc69
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@@ -57,12 +59,14 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_10
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-https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.2.0-h338b0a0_5.conda#a6be13181cb66a78544b1d5f7bac97d0
+https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.2.0-h9eb54c0_7.conda#57f0fcb5d432d5f98be5705e2bf65352
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_7.conda#1b84f26d9f4f6026e179e7805d5a15cd
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-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.2-h2797004_0.conda#866983a220e27a80cb75e85cb30466a1
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.3-h2797004_0.conda#b3316cbe90249da4f8e84cd66e1cc55b
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@@ -72,31 +76,32 @@ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47
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-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
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diff --git a/deploy/conda/env/lock/rnasum-osx-64.lock b/deploy/conda/env/lock/rnasum-osx-64.lock
index e50053a9..40b6c813 100644
--- a/deploy/conda/env/lock/rnasum-osx-64.lock
+++ b/deploy/conda/env/lock/rnasum-osx-64.lock
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+https://conda.anaconda.org/conda-forge/osx-64/libgfortran-5.0.0-13_2_0_h97931a8_3.conda#0b6e23a012ee7a9a5f6b244f5a92c1d5
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-https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-21_osx64_openblas.conda#23286066c595986aa0df6452a8416c08
+https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-22_osx64_openblas.conda#b80966a8c8dd0b531f8e65f709d732e8
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-https://conda.anaconda.org/conda-forge/osx-64/poppler-22.12.0-h6e9091c_1.conda#1d8cbcffea2c5ac4b315b06e0d48cbf7
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+https://conda.anaconda.org/conda-forge/osx-64/liblapack-3.9.0-22_osx64_openblas.conda#f21b282ff7ba14df6134a0fe6ab42b1b
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-https://conda.anaconda.org/conda-forge/osx-64/pango-1.50.14-hbd9bf65_0.conda#7de54d83e9c685b742e0a4d81b271de0
+https://conda.anaconda.org/conda-forge/osx-64/harfbuzz-6.0.0-h08f8713_0.conda#3852d6ef7b77da3e81074a8e487e7df5
+https://conda.anaconda.org/conda-forge/osx-64/poppler-22.12.0-h6e9091c_1.conda#1d8cbcffea2c5ac4b315b06e0d48cbf7
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+https://conda.anaconda.org/conda-forge/osx-64/pango-1.50.14-hbd9bf65_0.conda#7de54d83e9c685b742e0a4d81b271de0
 https://conda.anaconda.org/conda-forge/noarch/compiler-rt_osx-64-16.0.1-h613da45_0.conda#f276c02406940cd541b159f18a349dde
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 https://conda.anaconda.org/conda-forge/osx-64/clang_osx-64-16.0.1-hac0a0c4_1.conda#fe62ac2612b93dab371096301103d128
@@ -260,4 +267,4 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-biomart-2.50.0-r41hdfd78
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomicfeatures-1.46.1-r41hdfd78af_0.tar.bz2#749e6d8ea358fe4dfa6cc0b44b2306a6
 https://conda.anaconda.org/bioconda/noarch/bioconductor-edaseq-2.28.0-r41hdfd78af_0.tar.bz2#205da7c530172b1ecd74d636ae13dadf
 https://conda.anaconda.org/bioconda/noarch/bioconductor-ensembldb-2.18.1-r41hdfd78af_0.tar.bz2#2fd83dc07453cd129ca8b087284ade64
-https://conda.anaconda.org/umccr/noarch/r-rnasum-0.6.5-r41_0.tar.bz2#edd34c7ad0a5611793ac00026c1d25c5
+https://conda.anaconda.org/umccr/noarch/r-rnasum-1.0.0-r41_0.tar.bz2#c6e1c066ea2e8e5e05ae37fe0c5f6768
diff --git a/deploy/conda/env/yaml/rnasum.yaml b/deploy/conda/env/yaml/rnasum.yaml
index f050250d..83de1c68 100644
--- a/deploy/conda/env/yaml/rnasum.yaml
+++ b/deploy/conda/env/yaml/rnasum.yaml
@@ -6,4 +6,4 @@ channels:
   - bioconda
 
 dependencies:
-  - r-rnasum ==0.6.5 # versioned by bump2version
+  - r-rnasum ==1.0.0 # versioned by bump2version
diff --git a/deploy/conda/recipe/meta.yaml b/deploy/conda/recipe/meta.yaml
index 010caba6..c6a325ba 100644
--- a/deploy/conda/recipe/meta.yaml
+++ b/deploy/conda/recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-rnasum
-  version: 0.6.5 # bump2version
+  version: 1.0.0 # bump2version
 
 source:
   path: ../../../