Remove duplicate tests

.github/workflows/release.yaml

@@ -54,136 +54,4 @@ jobs:
           asset_path: ./geneshot.results.tar.gz
           asset_name: geneshot.results.tar.gz
           asset_content_type: application/gzip
-
-
-  no_preprocessing:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: 0
-    steps:
-      - uses: actions/checkout@v1
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Free disk space
-        run: |
-          sudo swapoff -a
-          sudo rm -f /swapfile
-          sudo apt clean
-          docker rmi $(docker image ls -aq)
-          df -h
-      - name:  Run geneshot
-        run: |
-          NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest --nopreprocess
-      - name:  Validate results
-        run: |
-          docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
-
-  add_formula:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: 0
-    steps:
-      - uses: actions/checkout@v1
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Free disk space
-        run: |
-          sudo swapoff -a
-          sudo rm -f /swapfile
-          sudo apt clean
-          docker rmi $(docker image ls -aq)
-          df -h
-      - name:  Run geneshot
-        run: |
-          NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest
-      - name:  Download annotations
-        run: |
-          wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog_proteins.dmnd && wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog.db
-      - name:  Add annotations
-        run: |
-          NXF_VER=20.04.1 nextflow run run_annotations.nf -c nextflow.config -profile testing --input_hdf output/geneshot.results.hdf5 --gene_fasta output/ref/genes.fasta.gz --output_folder output_with_annotations --output_hdf geneshot.results.hdf5 --eggnog_db eggnog.db --eggnog_dmnd eggnog_proteins.dmnd  -w work/ -with-docker ubuntu:latest
-      - name:  Run corncob
-        run: |
-          NXF_VER=20.04.1 nextflow run run_corncob.nf -c nextflow.config -profile testing --input_hdf output_with_annotations/geneshot.results.hdf5 --input_folder output/ --output_folder output_with_corncob --output_prefix geneshot --formula "label1,label2" -w work/ -with-docker ubuntu:latest
-      - name:  Validate results
-        run: |
-          docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output_with_corncob/geneshot.label1_label2.corncob.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
-  
-  no_assembly:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: 0
-    steps:
-      - uses: actions/checkout@v1
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Free disk space
-        run: |
-          sudo swapoff -a
-          sudo rm -f /swapfile
-          sudo apt clean
-          docker rmi $(docker image ls -aq)
-          df -h
-      - name:  Run geneshot
-        run: |
-          NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz
-      - name:  Validate results
-        run: |
-          docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly --check-corncob
-
-  eggnog:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: 0
-    steps:
-      - uses: actions/checkout@v1
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Free disk space
-        run: |
-          sudo swapoff -a
-          sudo rm -f /swapfile
-          sudo apt clean
-          docker rmi $(docker image ls -aq)
-          df -h
-      - name:  Download annotations
-        run: |
-          wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog_proteins.dmnd && wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog.db
-      - name:  Run geneshot
-        run: |
-          NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.15 -w work/ -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz --eggnog_dmnd eggnog_proteins.dmnd --eggnog_db eggnog.db --taxonomic_dmnd false
-      - name:  Validate results
-        run: |
-          docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly --check-corncob
-
-  composition:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: 0
-    steps:
-      - uses: actions/checkout@v1
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Free disk space
-        run: |
-          sudo swapoff -a
-          sudo rm -f /swapfile
-          sudo apt clean
-          docker rmi $(docker image ls -aq)
-          df -h
-      - name:  Run geneshot
-        run: |
-          NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --distance_threshold 0.5 -w work/ -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz --composition --taxonomic_dmnd false --eggnog_db false --eggnog_dmnd false
-      - name:  Validate results
-        run: |
-          docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly
+