From f1e00f5552b835cb29e37d984fd3bf13c6518192 Mon Sep 17 00:00:00 2001 From: Foivos Gypas Date: Sun, 22 Dec 2024 20:31:08 +0100 Subject: [PATCH] Fix CI --- .github/workflows/ci.yml | 5 +++++ .github/workflows/docs.yml | 3 ++- tests/input_files/samples_docker.tsv | 3 --- 3 files changed, 7 insertions(+), 4 deletions(-) delete mode 100644 tests/input_files/samples_docker.tsv diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e1b9c19..1d12522 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,6 +32,7 @@ jobs: activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with root. packages run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml @@ -80,6 +81,7 @@ jobs: activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with root. packages run: | @@ -125,6 +127,7 @@ jobs: activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with root. packages run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml @@ -162,6 +165,7 @@ jobs: activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with root. packages run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml @@ -199,6 +203,7 @@ jobs: activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with dev. packages run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 7cb1c88..bb90f8d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -21,13 +21,14 @@ jobs: uses: conda-incubator/setup-miniconda@v3 with: python-version: "3.10" - mamba-version: "*" + mamba-version: "1" channels: conda-forge channel-priority: true auto-update-conda: false activate-environment: zarp environment-file: install/environment.yml auto-activate-base: false + conda-remove-defaults: true - name: Update zarp env with root. packages run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml diff --git a/tests/input_files/samples_docker.tsv b/tests/input_files/samples_docker.tsv deleted file mode 100644 index f1c1ee7..0000000 --- a/tests/input_files/samples_docker.tsv +++ /dev/null @@ -1,3 +0,0 @@ -sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf genome sd mean libtype fq1_polya_3p fq1_polya_5p fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p -synthetic_10_reads_paired_synthetic_10_reads_paired pe data/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens data/annotation.gtf data/genome.fa 100 250 ISF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX data/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT -synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se data/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens data/annotation.gtf data/genome.fa 100 250 SF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX