diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 6c4e157..c5edf22 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -28,7 +28,7 @@ jobs: - name: Install nextflow uses: nf-core/setup-nextflow@v2 with: - version: "24.10.2" + version: "24.04.4" - name: Install dependencies run: | python -m pip install --upgrade pip setuptools diff --git a/subworkflows/local/workflows.nf b/subworkflows/local/workflows.nf index 2f55001..bce5179 100644 --- a/subworkflows/local/workflows.nf +++ b/subworkflows/local/workflows.nf @@ -787,7 +787,7 @@ workflow VC { vc_ffpe_tonly=vc_ffpe_tonly |concat(varscan_tonly_ffpe_out) } } - + } //Combine All Variants Using VCF -> Annotate if (call_list.size()>1){ @@ -814,7 +814,8 @@ workflow VC { | annotvep_tonly_combined_ffpe } } - + + if("sage" in call_list){ somaticcall_input=sage_in }else if("mutect2" in call_list){ @@ -824,7 +825,8 @@ workflow VC { }else{ somaticcall_input=Channel.empty() } - } + + emit: somaticcall_input @@ -1245,11 +1247,11 @@ workflow INPUT_BAM { bamwithsample=baminput2.combine(sample_sheet,by:0).map{it.swap(3,0)}.combine(baminputonly,by:0).map{it.swap(3,0)} | view() - } else { + }else{ bamwithsample=baminputonly.combine(sample_sheet,by:0).map{it.swap(3,0)}.combine(baminputonly,by:0).map{it.swap(3,0)} - |view() - - } + | view() + } + bambyinterval_norm=bamwithsample | map {tumo,tubam,tbai,norm,norbam,norbai -> tuple(norm,norbam,norbai)} bambyinterval_tum=bamwithsample