Merge pull request #10 from LUMC/develop
Full rewrite of the pipeline
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- envs/multiqc.yml 0 additions, 80 deletionsenvs/multiqc.yml
- envs/picard.yml 0 additions, 21 deletionsenvs/picard.yml
- envs/samtools.yml 0 additions, 16 deletionsenvs/samtools.yml
- envs/seqtk.yml 0 additions, 16 deletionsenvs/seqtk.yml
- envs/sickle.yml 0 additions, 8 deletionsenvs/sickle.yml
- envs/tabix.yml 0 additions, 9 deletionsenvs/tabix.yml
- envs/vcfstats.yml 0 additions, 43 deletionsenvs/vcfstats.yml
- img/rulegraph.svg 262 additions, 426 deletionsimg/rulegraph.svg
- requirements-dev.txt 0 additions, 2 deletionsrequirements-dev.txt
- requirements.txt 0 additions, 3 deletionsrequirements.txt
- slurm-test/cluster.yaml 7 additions, 0 deletionsslurm-test/cluster.yaml
- slurm-test/config.yaml 8 additions, 0 deletionsslurm-test/config.yaml
- src/collect_stats.py 34 additions, 72 deletionssrc/collect_stats.py
- src/cutadapt_summary.py 65 additions, 0 deletionssrc/cutadapt_summary.py
- src/fastq-count.py 0 additions, 133 deletionssrc/fastq-count.py
- src/fastqc_stats.py 0 additions, 168 deletionssrc/fastqc_stats.py
- src/merge_stats.py 101 additions, 19 deletionssrc/merge_stats.py
- src/safe_fastqc.sh 0 additions, 38 deletionssrc/safe_fastqc.sh
- src/seqtk.sh 0 additions, 44 deletionssrc/seqtk.sh
- src/stats_to_tsv.py 10 additions, 33 deletionssrc/stats_to_tsv.py
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