diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
index 58ef7e41..633dc3e7 100644
--- a/.github/skip_nf_test.json
+++ b/.github/skip_nf_test.json
@@ -17,6 +17,8 @@
         "modules/msk/snppileup",
         "modules/msk/netmhcstabpan",
         "modules/msk/genomenexus/annotationpipeline",
+        "modules/msk/salmon/index",
+        "modules/msk/salmon/quant",
         "modules/msk/genomenexus/vcf2maf",
         "modules/msk/rediscoverte",
         "modules/msk/netmhcpan4",
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
deleted file mode 100644
index c53d77b7..00000000
--- a/.github/workflows/pytest-workflow.yml
+++ /dev/null
@@ -1,239 +0,0 @@
-name: Run pytest-workflow
-on:
-  push:
-    branches:
-      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
-      - "renovate/**" # branches Renovate creates
-  pull_request:
-    branches: [main, develop]
-  merge_group:
-    types: [checks_requested]
-    branches: [main, develop]
-  workflow_dispatch: {}
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-env:
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.2"
-
-jobs:
-  pytest-changes:
-    name: pytest-changes
-    runs-on: ubuntu-latest
-    outputs:
-      tags: ${{ steps.filter.outputs.changes }}
-      modules: ${{ steps.tags.outputs.modules }}
-      subworkflows: ${{ steps.tags.outputs.subworkflows }}
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 2 # To retrieve the preceding commit.
-
-      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-          token: ""
-
-      - name: Fetch module tags
-        id: tags
-        run: |
-          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
-          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
-
-      - name: debug
-        run: |
-          echo ${{ steps.tags.outputs.modules }}
-          echo ${{ steps.tags.outputs.subworkflows }}
-
-  pytest:
-    runs-on: ubuntu-latest
-    name: pytest
-    needs: [pytest-changes]
-    if: needs.pytest-changes.outputs.tags != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
-        profile: [conda, docker, singularity]
-        exclude:
-          - tags: "nf-test"
-          - profile: "conda"
-            tags: gbcms
-          - profile: "conda"
-            tags: polysolver
-          - profile: "conda"
-            tags: snppileup
-          - profile: "conda"
-            tags: facets
-          - profile: "conda"
-            tags: mutect1
-          - profile: "conda"
-            tags: phylowgs/createinput
-          - profile: "conda"
-            tags: phylowgs/parsecnvs
-          - profile: "conda"
-            tags: phylowgs/multievolve
-          - profile: "conda"
-            tags: phylowgs/writeresults
-          - profile: "conda"
-            tags: netmhcpan4
-          - profile: "conda"
-            tags: neoantigeninput
-          - profile: "conda"
-            tags: neoantigenediting/aligntoIEDB
-          - profile: "conda"
-            tags: neoantigenediting/computeFitness
-          - profile: "conda"
-            tags: subworkflows/neoantigen_editing
-          - profile: "conda"
-            tags: subworkflows/phylowgs
-          - profile: "conda"
-            tags: netmhcstabpan
-          - profile: "conda"
-            tags: ppflagfixer
-          - profile: "conda"
-            tags: neoantigenutils/generatemutfasta
-          - profile: "conda"
-            tags: neoantigenutils/formatnetmhcpan
-          - profile: "conda"
-            tags: neoantigenutils/generatehlastring
-          - profile: "conda"
-            tags: neoantigenutils/neoantigeninput
-          - profile: "conda"
-            tags: subworkflows/netmhcstabandpan
-          - profile: "conda"
-            tags: salmon/index
-          - profile: "conda"
-            tags: genomenexus/vcf2maf
-          - profile: "conda"
-            tags: genomenexus/annotationpipeline
-          - profile: "conda"
-            tags: ppflagfixer
-          - profile: "conda"
-            tags: pvmaf/tagtraceback
-          - profile: "conda"
-            tags: pvmaf/concat
-          - profile: "conda"
-            tags: genotypevariants/all
-          - profile: "conda"
-            tags: subworkflows/traceback
-          - profile: "conda"
-            tags: salmon/index
-          - profile: "conda"
-            tags: subworkflows/genome_nexus
-          - profile: "conda"
-            tags: salmon/quant
-          - profile: "conda"
-            tags: rediscoverte
-          - profile: "conda"
-            tags: neosv
-          - profile: "conda"
-            tags: netmhc3
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4
-        id: cache-pip-pytest
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pytest
-          restore-keys: |
-            ${{ runner.os }}-pip-pytest
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow cryptography
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: ${{ env.NXF_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
-        with:
-          auto-update-conda: true
-          conda-solver: libmamba
-          conda-remove-defaults: true
-
-      # Test the module
-      - name: Run pytest-workflow
-        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt-get update > /dev/null
-          sudo apt-get install bat > /dev/null
-          batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err}
-
-      - name: Setting global variables
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        id: parsed
-        with:
-          script: |
-            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
-          result-encoding: string
-
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
-        with:
-          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
-          path: |
-            /home/ubuntu/pytest_workflow_*/*/.nextflow.log
-            /home/ubuntu/pytest_workflow_*/*/log.out
-            /home/ubuntu/pytest_workflow_*/*/log.err
-            /home/ubuntu/pytest_workflow_*/*/work
-            !/home/ubuntu/pytest_workflow_*/*/work/conda
-            !/home/ubuntu/pytest_workflow_*/*/work/singularity
-            !${{ github.workspace }}/.singularity
-
-  confirm-pass:
-    runs-on: ubuntu-latest
-    needs: [pytest-changes, pytest]
-    if: always()
-    steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
-      - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: debug-print
-        if: always()
-        run: |
-          echo "toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/modules/msk/netmhc3/meta.yml b/modules/msk/netmhc3/meta.yml
index 9fdca613..53115204 100644
--- a/modules/msk/netmhc3/meta.yml
+++ b/modules/msk/netmhc3/meta.yml
@@ -43,7 +43,7 @@ input:
         type: string
         description:
           Allows netmhc to run in parallel. Should be 'MUT' or 'WT', it
-          will kick off two jobs. make a Channel.Of('MUT','WT') outside the module as
+          will kick off two jobs. make a channel.Of('MUT','WT') outside the module as
           an input. Running them in series is kicked off by putting in anything other
           than MUT or WT.
         pattern: "WT,MUT"
diff --git a/modules/msk/netmhcpan4/meta.yml b/modules/msk/netmhcpan4/meta.yml
index da25d9d0..511ef1ee 100644
--- a/modules/msk/netmhcpan4/meta.yml
+++ b/modules/msk/netmhcpan4/meta.yml
@@ -43,7 +43,7 @@ input:
         type: string
         description:
           Allows netmhcpan to run in parallel. Should be 'MUT' or 'WT', it
-          will kick off two jobs. make a Channel.Of('MUT','WT') outside the module as
+          will kick off two jobs. make a channel.Of('MUT','WT') outside the module as
           an input. Running them in series is kicked off by putting in anything other
           than MUT or WT.
         pattern: "WT,MUT"
diff --git a/modules/msk/netmhcstabpan/meta.yml b/modules/msk/netmhcstabpan/meta.yml
index d9bc3dc6..d84cd8e9 100644
--- a/modules/msk/netmhcstabpan/meta.yml
+++ b/modules/msk/netmhcstabpan/meta.yml
@@ -43,7 +43,7 @@ input:
         type: string
         description:
           Allows netmhcstabpan to run in parallel. Should be 'MUT' or 'WT',
-          it will kick off two jobs. make a Channel.Of('MUT','WT') outside the module
+          it will kick off two jobs. make a channel.Of('MUT','WT') outside the module
           as an input. Running them in series is kicked off by putting in anything other
           than MUT or WT.
         pattern: "WT,MUT"
diff --git a/modules/msk/salmon/quant/tests/main.nf.test b/modules/msk/salmon/quant/tests/main.nf.test
index 059bd378..d2cce8c7 100644
--- a/modules/msk/salmon/quant/tests/main.nf.test
+++ b/modules/msk/salmon/quant/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test', single_end: true ], // meta map
                     [ file(params.test_data_mskcc['rediscoverte']['input_R1_fq_gz'], checkIfExists: true) ]
                 ])
@@ -53,7 +53,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test', single_end: true ], // meta map
                     [ file('input_R1_fq_gz') ]
                 ])
diff --git a/subworkflows/msk/generate_mutated_peptides/main.nf b/subworkflows/msk/generate_mutated_peptides/main.nf
index ed9cf6f1..54dc99cb 100644
--- a/subworkflows/msk/generate_mutated_peptides/main.nf
+++ b/subworkflows/msk/generate_mutated_peptides/main.nf
@@ -15,7 +15,7 @@ workflow GENERATE_MUTATED_PEPTIDES {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     ch_maf = ch_maf_hla_sv
                 .map{
diff --git a/subworkflows/msk/generate_mutated_peptides/tests/main.nf.test b/subworkflows/msk/generate_mutated_peptides/tests/main.nf.test
index 5c43d73c..2c76633c 100644
--- a/subworkflows/msk/generate_mutated_peptides/tests/main.nf.test
+++ b/subworkflows/msk/generate_mutated_peptides/tests/main.nf.test
@@ -20,25 +20,25 @@ nextflow_workflow {
             workflow {
                 """
 
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['somatic_filtered_maf'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['winners_hla_txt'], checkIfExists: true),
                     ])
 
-                input[1] = Channel.value(
+                input[1] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['fa_gzip'], checkIfExists: true)
                     )
 
-                input[2] = Channel.value(
+                input[2] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['gff3'], checkIfExists: true)
                     )
 
-                input[3] = Channel.value(
+                input[3] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['gtf'], checkIfExists: true)
                     )
 
-                input[4] = Channel.value(
+                input[4] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['cdna'], checkIfExists: true)
                     )
 
@@ -64,26 +64,26 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['somatic_filtered_maf'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['winners_hla_txt'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['sv_filtered_bedpe'], checkIfExists: true)
                     ])
 
-                input[1] = Channel.value(
+                input[1] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['fa_gzip'], checkIfExists: true)
                     )
 
-                input[2] = Channel.value(
+                input[2] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['small_test_chr2and16']['gff3'], checkIfExists: true)
                     )
 
-                input[3] = Channel.value(
+                input[3] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['gtf'], checkIfExists: true)
                     )
 
-                input[4] = Channel.value(
+                input[4] = channel.value(
                     file(params.test_data_mskcc['neoantigen']['cdna'], checkIfExists: true)
                     )
 
@@ -114,26 +114,26 @@ nextflow_workflow {
             workflow {
                 """
 
-                input[0] = Channel.of([
+                input[0] = channel.of([
                     [ id:'test', single_end:false ], // meta map
                     file('somatic_filtered_maf', checkIfExists: false),
                     file('winners_hla_txt', checkIfExists: false),
                     file('sv_filtered_bedpe', checkIfExists: false)
                     ])
 
-                input[1] = Channel.value(
+                input[1] = channel.value(
                     file('fa_gzip', checkIfExists: false)
                     )
 
-                input[2] = Channel.value(
+                input[2] = channel.value(
                     file('gff3', checkIfExists: false)
                     )
 
-                input[3] = Channel.value(
+                input[3] = channel.value(
                     file('gtf', checkIfExists: false)
                     )
 
-                input[4] = Channel.value(
+                input[4] = channel.value(
                     file('cdna', checkIfExists: false)
                     )
 
diff --git a/subworkflows/msk/genome_nexus/main.nf b/subworkflows/msk/genome_nexus/main.nf
index 1aaaeb42..6aef3983 100644
--- a/subworkflows/msk/genome_nexus/main.nf
+++ b/subworkflows/msk/genome_nexus/main.nf
@@ -8,7 +8,7 @@ workflow GENOME_NEXUS {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
 
     GENOMENEXUS_VCF2MAF ( ch_vcf )
diff --git a/subworkflows/msk/genome_nexus/meta.yml b/subworkflows/msk/genome_nexus/meta.yml
index e1d6dc2a..e624dab1 100644
--- a/subworkflows/msk/genome_nexus/meta.yml
+++ b/subworkflows/msk/genome_nexus/meta.yml
@@ -24,7 +24,7 @@ output:
   - maf:
       type: file
       description: |
-        Channel containing output converted and annotated MAF file
+        channel containing output converted and annotated MAF file
         Structure: [ val(meta), path(maf) ]
 
   - versions:
diff --git a/subworkflows/msk/neoantigen_editing/main.nf b/subworkflows/msk/neoantigen_editing/main.nf
index 33747289..bf44eca4 100644
--- a/subworkflows/msk/neoantigen_editing/main.nf
+++ b/subworkflows/msk/neoantigen_editing/main.nf
@@ -10,7 +10,7 @@ workflow NEOANTIGEN_EDITING {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     NEOANTIGENEDITING_ALIGNTOIEDB (neoantigenInput_ch, iedbfasta)
     ch_versions = ch_versions.mix(NEOANTIGENEDITING_ALIGNTOIEDB.out.versions.first())
diff --git a/subworkflows/msk/neoantigen_editing/meta.yml b/subworkflows/msk/neoantigen_editing/meta.yml
index 9f1cd646..e70b49d5 100644
--- a/subworkflows/msk/neoantigen_editing/meta.yml
+++ b/subworkflows/msk/neoantigen_editing/meta.yml
@@ -25,7 +25,7 @@ output:
   - annotated_output:
       type: file
       description: |
-        Channel containing annpotated json output with neoantigen quality
+        channel containing annpotated json output with neoantigen quality
         Structure: [ val(meta), [ annotated_json ] ]
       pattern: "*.json"
   - versions:
diff --git a/subworkflows/msk/neoantigen_editing/tests/main.nf.test b/subworkflows/msk/neoantigen_editing/tests/main.nf.test
index 774875ac..5dcc23c4 100644
--- a/subworkflows/msk/neoantigen_editing/tests/main.nf.test
+++ b/subworkflows/msk/neoantigen_editing/tests/main.nf.test
@@ -19,11 +19,11 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map,
                     file(params.test_data_mskcc['neoantigen']['patient_data'], checkIfExists: true)
                     ])
-                input[1] = Channel.value(file(params.test_data_mskcc['neoantigen']['iedb']['iedb_fasta'], checkIfExists: true))
+                input[1] = channel.value(file(params.test_data_mskcc['neoantigen']['iedb']['iedb_fasta'], checkIfExists: true))
 
                 """
             }
@@ -49,11 +49,11 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map,
                     file('patient_data')
                     ])
-                input[1] = Channel.value(file('iedb_fasta'))
+                input[1] = channel.value(file('iedb_fasta'))
 
                 """
             }
diff --git a/subworkflows/msk/netmhcstabandpan/main.nf b/subworkflows/msk/netmhcstabandpan/main.nf
index 144c0afc..f8f73a9a 100644
--- a/subworkflows/msk/netmhcstabandpan/main.nf
+++ b/subworkflows/msk/netmhcstabandpan/main.nf
@@ -12,7 +12,7 @@ workflow NETMHCSTABANDPAN {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     ch_netmhcinput = createNETMHCInput(ch_fasta_and_hla, ch_sv_fasta)
 
@@ -20,7 +20,7 @@ workflow NETMHCSTABANDPAN {
 
     ch_versions = ch_versions.mix(NETMHCSTABPAN.out.versions)
 
-    merged_pan_and_stab = Channel.empty()
+    merged_pan_and_stab = channel.empty()
 
     merged_pan_and_stab = merged_pan_and_stab.mix( NETMHCSTABPAN.out.netmhcstabpanoutput )
 
diff --git a/subworkflows/msk/netmhcstabandpan/meta.yml b/subworkflows/msk/netmhcstabandpan/meta.yml
index 3c3dc921..376205d3 100644
--- a/subworkflows/msk/netmhcstabandpan/meta.yml
+++ b/subworkflows/msk/netmhcstabandpan/meta.yml
@@ -28,7 +28,7 @@ output:
   - tsv:
       type: file
       description: |
-        Channel containing TSV files
+        channel containing TSV files
         Structure: [ val(meta), path(tsv) ]
       pattern: "*.tsv"
   - versions:
diff --git a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test
index f72b54a8..5cf809f1 100644
--- a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test
+++ b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test
@@ -18,14 +18,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sequence_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sequence_fa'], checkIfExists: true),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sv_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sv_fa'], checkIfExists: true)
@@ -58,14 +58,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sequence_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sequence_fa'], checkIfExists: true),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sv_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sv_fa'], checkIfExists: true)
@@ -96,14 +96,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sequence_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sequence_fa'], checkIfExists: true),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     [],
                     []
@@ -132,14 +132,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['MUT_sequence_fa'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['WT_sequence_fa'], checkIfExists: true),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     [],
                     []
@@ -169,14 +169,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file('MUT_sequence_fa', checkIfExists: false),
                     file('WT_sequence_fa', checkIfExists: false),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file('MUT_sv_fa', checkIfExists: false),
                     file('WT_sv_fa', checkIfExists: false)
@@ -212,14 +212,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file('MUT_sequence_fa', checkIfExists: false),
                     file('WT_sequence_fa', checkIfExists: false),
                     "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
                     ])
 
-                input[1] = Channel.value([
+                input[1] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file('MUT_sv_fa', checkIfExists: false),
                     file('WT_sv_fa', checkIfExists: false)
diff --git a/subworkflows/msk/phylowgs/main.nf b/subworkflows/msk/phylowgs/main.nf
index 2ce0b375..6c650cf3 100644
--- a/subworkflows/msk/phylowgs/main.nf
+++ b/subworkflows/msk/phylowgs/main.nf
@@ -10,7 +10,7 @@ workflow PHYLOWGS {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     ch_genelevel = ch_input_maf_and_genelevel
                         .map{
diff --git a/subworkflows/msk/phylowgs/tests/main.nf.test b/subworkflows/msk/phylowgs/tests/main.nf.test
index 7fa9052c..f6cc609e 100644
--- a/subworkflows/msk/phylowgs/tests/main.nf.test
+++ b/subworkflows/msk/phylowgs/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file(params.test_data_mskcc['neoantigen']['unfilteredmaf'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['facets_hisens_cncf_txt'], checkIfExists: true)
@@ -49,7 +49,7 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.value([
+                input[0] = channel.value([
                     [ id:'test', single_end:false ], // meta map
                     file('unfilteredmaf'),
                     file('facets_gene_level_txt')
diff --git a/subworkflows/msk/traceback/main.nf b/subworkflows/msk/traceback/main.nf
index 7123932a..13eb3aec 100644
--- a/subworkflows/msk/traceback/main.nf
+++ b/subworkflows/msk/traceback/main.nf
@@ -16,7 +16,7 @@ workflow TRACEBACK {
     main:
 
     // declare versions channel
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     // Concat Input Mafs
     PVMAFCONCAT_INITIAL(mafs)
diff --git a/subworkflows/msk/traceback/meta.yml b/subworkflows/msk/traceback/meta.yml
index e5150699..54c9ffc0 100644
--- a/subworkflows/msk/traceback/meta.yml
+++ b/subworkflows/msk/traceback/meta.yml
@@ -18,14 +18,14 @@ input:
       type: channel
       description: |
         An input channel containing impact or access bams files:
-        impact: Channel.of([patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], [])
-        access: Channel.of([patient:null, id:'sample'], [], [], duplex.bam, duplex.bam.bai, simplex.bam, simplex.bam.bai])
+        impact: channel.of([patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], [])
+        access: channel.of([patient:null, id:'sample'], [], [], duplex.bam, duplex.bam.bai, simplex.bam, simplex.bam.bai])
       pattern: "*.{bam/cram/sam}"
   - mafs:
       type: channel
       description: |
         An input channel containing maf files
-        Structure: // channel: Channel.of([[patient:null, id:'sample'], [maf1,...,maf2]], [[patient:null, id:'sample'], [maf1,...,maf2] ]])
+        Structure: // channel: channel.of([[patient:null, id:'sample'], [maf1,...,maf2]], [[patient:null, id:'sample'], [maf1,...,maf2] ]])
       pattern: "*.{maf,txt,tsv}"
   - fasta:
       type: file
diff --git a/subworkflows/msk/traceback/tests/main.nf.test b/subworkflows/msk/traceback/tests/main.nf.test
index 72e50bc4..529e0dc0 100644
--- a/subworkflows/msk/traceback/tests/main.nf.test
+++ b/subworkflows/msk/traceback/tests/main.nf.test
@@ -17,14 +17,14 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = Channel.of(
+                input[0] = channel.of(
                     [[id:'sample1', patient: 'patient1'],file('sample1.bam'),file('sample1.bam.bai'),[], [], [], []],[[id:'sample2', patient:'patient2'], [], [],
                     file('sample2-duplex.bam'),
                     file('sample2-duplex.bam.bai'),
                     file('sample2-simplex.bam'),file('sample2-simplex.bam.bai')
                     ])
 
-                input[1] = Channel.of(
+                input[1] = channel.of(
                     [[patient: 'patient1'],
                     [file('patient1.txt'),]
                     ],