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Update slurm cluster config files for new exectutor, fix #51, fix #54 #100

Update slurm cluster config files for new exectutor, fix #51, fix #54

Update slurm cluster config files for new exectutor, fix #51, fix #54 #100

Triggered via push December 10, 2024 01:11
Status Cancelled
Total duration 1m 48s
Artifacts 50

ci.yaml

on: push
Matrix: envs
Matrix: example
Matrix: test
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151 errors and 1 warning
envs (macos-12, micromamba)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
envs (macos-12, micromamba)
GitHub Actions has encountered an internal error when running your job.
envs (macos-12, mamba)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
envs (macos-12, mamba)
GitHub Actions has encountered an internal error when running your job.
test (macos-12, base)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
test (macos-12, base)
GitHub Actions has encountered an internal error when running your job.
example (macos-12)
The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see https://github.com/actions/runner-images/issues/10721
example (macos-12)
GitHub Actions has encountered an internal error when running your job.
envs (macos-13, mamba)
The run was canceled by @lczech.
envs (macos-13, mamba)
ENOENT: no such file or directory, lstat '/Users/runner/work/_temp/setup-micromamba/micromamba-shell'
envs (macos-13, mamba)
The operation was canceled.
envs (macos-13, micromamba)
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envs (macos-13, micromamba)
ENOENT: no such file or directory, lstat '/Users/runner/work/_temp/setup-micromamba/micromamba-shell'
envs (macos-13, micromamba)
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example (macos-13)
The run was canceled by @lczech.
example (macos-13)
ENOENT: no such file or directory, lstat '/Users/runner/work/_temp/setup-micromamba/micromamba-shell'
example (macos-13)
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test (macos-13, base)
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test (macos-13, base)
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test (macos-13, base)
Process completed with exit code 1.
test (macos-13, base)
ENOENT: no such file or directory, lstat '/Users/runner/work/_temp/setup-micromamba/micromamba-shell'
envs (ubuntu-24.04, mamba)
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envs (ubuntu-24.04, mamba)
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envs (ubuntu-22.04, mamba)
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envs (ubuntu-22.04, mamba)
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envs (ubuntu-20.04, mamba)
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envs (ubuntu-20.04, mamba)
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envs (ubuntu-20.04, micromamba)
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envs (ubuntu-20.04, micromamba)
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envs (ubuntu-24.04, micromamba)
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envs (ubuntu-24.04, micromamba)
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test (ubuntu-latest, calling-haplotypecaller-3, mamba)
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test (ubuntu-latest, calling-haplotypecaller-3, mamba)
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test (ubuntu-latest, calling-haplotypecaller-3, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/plotly-5.24.1-pyhd8ed1ab_1/site-packages/plotly-5.24.1.dist-info'
test (ubuntu-latest, calling-freebayes-2, mamba)
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test (ubuntu-latest, calling-freebayes-2, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/gcc_impl_linux-64-14.2.0-h6b349bd_1/bin'
test (ubuntu-latest, calling-freebayes-2, mamba)
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test (ubuntu-latest, mapping-bwa-mem2-1, mamba)
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test (ubuntu-latest, mapping-bwa-mem2-1, mamba)
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test (ubuntu-latest, mapping-bwa-mem2-1, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/damageprofiler-1.1-hdfd78af_2'
example (ubuntu-24.04)
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example (ubuntu-24.04)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/perl-5.32.1-7_hd590300_perl5/bin'
example (ubuntu-24.04)
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test (ubuntu-latest, calling-haplotypecaller-2, mamba)
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test (ubuntu-latest, calling-haplotypecaller-2, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/python-3.13.1-ha99a958_102_cp313/bin'
test (ubuntu-latest, calling-haplotypecaller-2, mamba)
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example (ubuntu-22.04)
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example (ubuntu-22.04)
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envs (ubuntu-22.04, micromamba)
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envs (ubuntu-22.04, micromamba)
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test (ubuntu-latest, calling-haplotypecaller-1, mamba)
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test (ubuntu-latest, calling-haplotypecaller-1, mamba)
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test (ubuntu-latest, trimming-fastp-1, mamba)
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test (ubuntu-latest, trimming-fastp-1, mamba)
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test (ubuntu-latest, trimming-fastp-1, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/perl-5.32.1-7_hd590300_perl5/bin'
example (ubuntu-20.04)
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example (ubuntu-20.04)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/ncurses-6.1-hf484d3e_1002'
example (ubuntu-20.04)
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test (ubuntu-latest, calling-bcftools-1, mamba)
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test (ubuntu-latest, calling-bcftools-1, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/blast-2.16.0-hc155240_3/lib/ncbi-blast+'
test (ubuntu-latest, calling-bcftools-1, mamba)
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test (ubuntu-latest, download, mamba)
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test (ubuntu-latest, download, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/picard-3.2.0-hdfd78af_0/share/picard-3.2.0-0'
test (ubuntu-latest, download, mamba)
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test (ubuntu-latest, duplicates-dedup-1, mamba)
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test (ubuntu-latest, duplicates-dedup-1, mamba)
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test (ubuntu-latest, duplicates-dedup-1, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs'
test (ubuntu-latest, trimming-adapterremoval-2, mamba)
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test (ubuntu-latest, trimming-adapterremoval-2, mamba)
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test (ubuntu-latest, hafpipe-2, mamba)
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test (ubuntu-latest, hafpipe-2, mamba)
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test (ubuntu-latest, hafpipe-2, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/gcc_impl_linux-64-14.2.0-h6b349bd_1/bin'
test (ubuntu-latest, trimming-skewer-2, mamba)
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test (ubuntu-latest, trimming-skewer-2, mamba)
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test (ubuntu-24.04, base)
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test (ubuntu-24.04, base)
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test (ubuntu-latest, base, mamba)
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test (ubuntu-latest, base, mamba)
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test (ubuntu-latest, mapping-bwa-aln-2, mamba)
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test (ubuntu-latest, mapping-bwa-aln-2, mamba)
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test (ubuntu-latest, trimming-seqprep-2, mamba)
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test (ubuntu-latest, trimming-seqprep-2, mamba)
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ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/r-base-4.4.2-h64c9cd0_0/lib/R/bin'
test (ubuntu-latest, trimming-adapterremoval-1, mamba)
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test (ubuntu-latest, trimming-adapterremoval-1, mamba)
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test (ubuntu-20.04, base)
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test (ubuntu-20.04, base)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/plotly-5.24.1-pyhd8ed1ab_1/site-packages/plotly/figure_factory'
test (ubuntu-20.04, base)
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test (ubuntu-22.04, base)
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test (ubuntu-22.04, base)
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test (ubuntu-22.04, base)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs'
test (ubuntu-latest, hafpipe-1, mamba)
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test (ubuntu-latest, hafpipe-1, mamba)
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test (ubuntu-latest, trimming-skewer-1, mamba)
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test (ubuntu-latest, trimming-skewer-1, mamba)
ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/python-tzdata-2024.2-pyhd8ed1ab_1/info'
test (ubuntu-latest, trimming-skewer-1, mamba)
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test (ubuntu-latest, calling-bcftools-4, mamba)
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test (ubuntu-latest, calling-freebayes-1, mamba)
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ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/r-bh-1.84.0_0-r43hc72bb7e_1/lib/R/library/BH/include/boost/serialization'
test (ubuntu-latest, trimming-seqprep-1, mamba)
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ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/plotly-5.24.1-pyhd8ed1ab_1/site-packages/plotly/graph_objs/choropleth'
test (ubuntu-latest, trimming-fastp-3, mamba)
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ENOTEMPTY: directory not empty, rmdir '/home/runner/micromamba/envs/grenepipe/pkgs/gcc_impl_linux-64-14.2.0-h6b349bd_1/bin'
test (ubuntu-latest, trimming-fastp-3, mamba)
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test (ubuntu-latest, calling-haplotypecaller-4, mamba)
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test (ubuntu-latest, calling-haplotypecaller-4, mamba)
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test (ubuntu-latest, mapping-bowtie2-1, mamba)
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test (ubuntu-latest, trimming-cutadapt-1, mamba)
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test (ubuntu-latest, mapping-bowtie2-1, mamba)
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test (ubuntu-latest, trimming-cutadapt-1, mamba)
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test (ubuntu-latest, mappings-table, mamba)
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test (ubuntu-latest, mappings-table, mamba)
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test (ubuntu-latest, calling-bcftools-3, mamba)
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test (ubuntu-latest, calling-bcftools-3, mamba)
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test (ubuntu-latest, trimming-none, mamba)
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test (ubuntu-latest, trimming-none, mamba)
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test (ubuntu-latest, mapping-bwa-aln-1, mamba)
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test (ubuntu-latest, mapping-bwa-aln-1, mamba)
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test (ubuntu-latest, trimming-cutadapt-2, mamba)
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test (ubuntu-latest, trimming-cutadapt-2, mamba)
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test (ubuntu-latest, trimming-adapterremoval-3, mamba)
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test (ubuntu-latest, trimming-adapterremoval-3, mamba)
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test (ubuntu-latest, trimming-fastp-2, mamba)
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test (ubuntu-latest, trimming-fastp-2, mamba)
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test (ubuntu-latest, hafpipe-4, mamba)
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test (ubuntu-latest, calling-bcftools-2, mamba)
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test (ubuntu-latest, hafpipe-3, mamba)
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test (ubuntu-latest, hafpipe-3, mamba)
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test (ubuntu-latest, mapping-bowtie2-2, mamba)
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test (ubuntu-latest, pileup-1, mamba)
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test (ubuntu-latest, pileup-1, mamba)
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test (ubuntu-latest, calling-freebayes-3, mamba)
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test (ubuntu-latest, mapping-bwa-mem-1, mamba)
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test (ubuntu-latest, mapping-bwa-mem-1, mamba)
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test (ubuntu-latest, mapping-bwa-aln-4, mamba)
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test (ubuntu-latest, mapping-bwa-mem2-2, mamba)
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example (macos-13)
No files were found with the provided path: example/run.log example/logs/ example/.snakemake/log/. No artifacts will be uploaded.

Artifacts

Produced during runtime
Name Size
logs-example-ubuntu-20.04
3.06 KB
logs-example-ubuntu-22.04
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logs-example-ubuntu-24.04
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logs-test-macos-13-base
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logs-test-ubuntu-20.04-base
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logs-test-ubuntu-22.04-base
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logs-test-ubuntu-24.04-base
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logs-test-ubuntu-latest-base
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logs-test-ubuntu-latest-calling-bcftools-1
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logs-test-ubuntu-latest-calling-bcftools-2
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logs-test-ubuntu-latest-calling-bcftools-3
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logs-test-ubuntu-latest-calling-bcftools-4
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logs-test-ubuntu-latest-calling-freebayes-1
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logs-test-ubuntu-latest-calling-freebayes-2
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logs-test-ubuntu-latest-calling-freebayes-3
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logs-test-ubuntu-latest-calling-haplotypecaller-1
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logs-test-ubuntu-latest-calling-haplotypecaller-2
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logs-test-ubuntu-latest-calling-haplotypecaller-3
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logs-test-ubuntu-latest-calling-haplotypecaller-4
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logs-test-ubuntu-latest-download
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logs-test-ubuntu-latest-duplicates-dedup-1
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logs-test-ubuntu-latest-duplicates-dedup-2
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logs-test-ubuntu-latest-hafpipe-1
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logs-test-ubuntu-latest-hafpipe-2
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logs-test-ubuntu-latest-hafpipe-3
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logs-test-ubuntu-latest-hafpipe-4
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logs-test-ubuntu-latest-mapping-bowtie2-1
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logs-test-ubuntu-latest-mapping-bowtie2-2
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logs-test-ubuntu-latest-mapping-bwa-aln-1
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logs-test-ubuntu-latest-mapping-bwa-aln-2
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logs-test-ubuntu-latest-mapping-bwa-aln-3
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logs-test-ubuntu-latest-mapping-bwa-aln-4
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logs-test-ubuntu-latest-mapping-bwa-mem-1
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logs-test-ubuntu-latest-mapping-bwa-mem2-1
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logs-test-ubuntu-latest-mapping-bwa-mem2-2
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logs-test-ubuntu-latest-mappings-table
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logs-test-ubuntu-latest-pileup-1
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logs-test-ubuntu-latest-trimming-adapterremoval-1
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logs-test-ubuntu-latest-trimming-adapterremoval-2
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logs-test-ubuntu-latest-trimming-adapterremoval-3
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logs-test-ubuntu-latest-trimming-cutadapt-1
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logs-test-ubuntu-latest-trimming-cutadapt-2
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logs-test-ubuntu-latest-trimming-fastp-1
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logs-test-ubuntu-latest-trimming-fastp-2
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logs-test-ubuntu-latest-trimming-fastp-3
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logs-test-ubuntu-latest-trimming-none
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logs-test-ubuntu-latest-trimming-seqprep-1
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logs-test-ubuntu-latest-trimming-seqprep-2
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logs-test-ubuntu-latest-trimming-skewer-1
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logs-test-ubuntu-latest-trimming-skewer-2
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