diff --git a/.github/workflows/titan-gc.yml b/.github/workflows/titan-gc.yml index b5b931c6..31ba0bc8 100644 --- a/.github/workflows/titan-gc.yml +++ b/.github/workflows/titan-gc.yml @@ -21,7 +21,7 @@ jobs: - name: Setup miniconda uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: titan-gc-cli + activate-environment: titan-gc auto-activate-base: false - name: Setup Titan CI Environment @@ -30,13 +30,13 @@ jobs: chmod 755 bin/* cp bin/* ${CONDA_PREFIX}/bin TITAN_GC_VERSION=$(grep "PHVG_Version=" tasks/task_versioning.wdl | sed -E 's/.*="PHVG v(.*)"/\1/') - export TITAN_GC_VERSION=$(TITAN_GC_VERSION) - TITAN_SHARE="${CONDA_PREFIX}/share/titan-gc-cli-${TITAN_GC_VERSION}" + echo "TITAN_GC_VERSION=${TITAN_GC_VERSION}" >> $GITHUB_ENV + TITAN_SHARE="${CONDA_PREFIX}/share/titan-gc-${TITAN_GC_VERSION}" mkdir -p ${TITAN_SHARE} mv conf/ tasks/ workflows/ ${TITAN_SHARE} - name: Environment Information - run: uname -a && env && titan-gc-cli -h + run: uname -a && env && titan-gc -h - name: Test Titan-GC Workflows run: | diff --git a/bin/titan-gc-cli b/bin/titan-gc similarity index 88% rename from bin/titan-gc-cli rename to bin/titan-gc index 8ec0ebdc..54f42e1e 100755 --- a/bin/titan-gc-cli +++ b/bin/titan-gc @@ -1,7 +1,7 @@ #! /bin/bash -# usage: titan-gc-cli [-h] [-i STR] [--inputs STR] [-o STR] [--outdir STR] [--options STR] [--verbose] +# usage: titan-gc [-h] [-i STR] [--inputs STR] [-o STR] [--outdir STR] [--options STR] [--verbose] # -# titan-gc-cli - Run Titan GC on a set of samples. +# titan-gc - Run Titan GC on a set of samples. # # required arguments: # -i STR, --inputs STR The JSON file to be used with Cromwell for inputs. @@ -18,23 +18,22 @@ OPTIONS="0" QUIET="0" PROFILE="docker" CONFIG="0" -VERSION="1.4.4" -TITAN_PATH=$(which titan-gc-cli | sed 's=bin/titan-gc-cli==') -TITAN_SHARE=${TITAN_PATH}/share/titan-gc-cli-${VERSION} +TITAN_PATH=$(which titan-gc | sed 's=bin/titan-gc==') +TITAN_SHARE=${TITAN_PATH}/share/titan-gc-${TITAN_GC_VERSION} CROMWELL_JAR=$(which cromwell | sed 's=bin/cromwell=share/cromwell/cromwell.jar=') LOG_LEVEL=ERROR SINGULARITY_CACHE="${HOME}/.singularity/titan-cache" CROMWELL_OPTS="${TITAN_SHARE}/conf/options.json" version() { - echo "titan-gc-cli ${VERSION}" + echo "titan-gc ${TITAN_GC_VERSION}" exit 0 } usage() { - echo "usage: titan-gc-cli [-h] [-i STR] [--inputs STR] [-o STR] [--outdir STR] [--options STR] [--quiet]" + echo "usage: titan-gc [-h] [-i STR] [--inputs STR] [-o STR] [--outdir STR] [--options STR] [--quiet]" echo "" - echo "titan-gc-cli - Run Titan GC on a set of samples." + echo "titan-gc - Run Titan GC on a set of samples." echo "" echo "required arguments:" echo " -i STR, --inputs STR The JSON file to be used with Cromwell for inputs." diff --git a/tests/workflows/titan-gc/test_clearlabs.yml b/tests/workflows/titan-gc/test_clearlabs.yml index 717c82bd..db09f8f4 100644 --- a/tests/workflows/titan-gc/test_clearlabs.yml +++ b/tests/workflows/titan-gc/test_clearlabs.yml @@ -1,5 +1,5 @@ - name: titan_clearlabs - command: titan-gc-cli -i titan/clearlabs.json -o titan/clearlabs + command: titan-gc -i titan/clearlabs.json -o titan/clearlabs tags: - titan_gc - titan_clearlabs diff --git a/tests/workflows/titan-gc/test_illumina_pe.yml b/tests/workflows/titan-gc/test_illumina_pe.yml index 81949f49..f52a19a8 100644 --- a/tests/workflows/titan-gc/test_illumina_pe.yml +++ b/tests/workflows/titan-gc/test_illumina_pe.yml @@ -1,5 +1,5 @@ - name: titan_illumina_pe - command: titan-gc-cli -i titan/illumina_pe.json -o titan/illumina_pe + command: titan-gc -i titan/illumina_pe.json -o titan/illumina_pe tags: - titan_gc - titan_illumina_pe diff --git a/tests/workflows/titan-gc/test_illumina_se.yml b/tests/workflows/titan-gc/test_illumina_se.yml index 02662ab2..f87dd3fc 100644 --- a/tests/workflows/titan-gc/test_illumina_se.yml +++ b/tests/workflows/titan-gc/test_illumina_se.yml @@ -1,5 +1,5 @@ - name: titan_illumina_se - command: titan-gc-cli -i titan/illumina_se.json -o titan/illumina_se + command: titan-gc -i titan/illumina_se.json -o titan/illumina_se tags: - titan_gc - titan_illumina_se diff --git a/tests/workflows/titan-gc/test_ont.yml b/tests/workflows/titan-gc/test_ont.yml index 3591f477..7b39eb1c 100644 --- a/tests/workflows/titan-gc/test_ont.yml +++ b/tests/workflows/titan-gc/test_ont.yml @@ -1,5 +1,5 @@ - name: titan_ont - command: titan-gc-cli -i titan/ont.json -o titan/ont + command: titan-gc -i titan/ont.json -o titan/ont tags: - titan_gc - titan_ont diff --git a/workflows/wf_titan_gc.wdl b/workflows/wf_titan_gc.wdl index 572547af..96946c26 100644 --- a/workflows/wf_titan_gc.wdl +++ b/workflows/wf_titan_gc.wdl @@ -25,7 +25,7 @@ workflow titan_gc { input { Array[parseJSON] samples - String pangolin_docker_image = "staphb/pangolin:3.1.3-pangolearn-2021-06-15" + String pangolin_docker_image = "staphb/pangolin:3.1.11-pangolearn-2021-08-09" } scatter (sample in samples) {