capturing sambamba/markdup log for MultiQC report #247

	name: pytest

	on: [pull_request, push]

	defaults:
	run:
	shell: bash -l {0}

	jobs:
	test_mRNA:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: snakePipes/shared/rules/envs/rna_seq.yaml
	activate-environment: snakepipes_RNAseq_environment_3.0
	condarc-file: .github/condarc.yml
	- name: create_starix
	run: \|
	gunzip -c tests/data/genomes/genome_chr17.fa.gz > genome_chr17.fa
	gunzip -c tests/data/genomes/genes_chr17.gtf.gz > genes_chr17.gtf
	STAR --runThreadN 4 --runMode genomeGenerate --genomeDir tests/data/mRNA_STAR --genomeFastaFiles genome_chr17.fa --sjdbGTFfile genes_chr17.gtf --sjdbOverhang 100 --genomeSAindexNbases 12
	- uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: .github/conda_ci.yml
	activate-environment: conda_ci
	condarc-file: .github/condarc.yml
	- name: Install snakePipes
	run: \|
	pip install .[actions]
	- name: pytest
	run: \|
	snakePipes config --tempDir /tmp --condaEnvDir ./
	snakePipes createEnvs --only CONDA_SHARED_ENV CONDA_RNASEQ_ENV
	pytest --verbosity=2 -rP tests/test_mRNA.py
	CI_jobcounts:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: .github/conda_ci.yml
	activate-environment: conda_ci
	condarc-file: .github/condarc.yml
	- name: Install snakePipes
	run: \|
	pip install .[actions]
	- name: pytest
	run: \|
	snakePipes config --tempDir /tmp --condaEnvDir ./
	pytest -n 4 --verbosity=2 -rP tests/test_jobcounts.py

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