mirror of
https://github.com/MillironX/nf-core_modules.git
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1455498152
* Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
101 lines
4.5 KiB
YAML
Executable file
101 lines
4.5 KiB
YAML
Executable file
- name: cnvkit batch test_cnvkit_hybrid
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command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c tests/config/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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files:
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- path: output/cnvkit/baits.antitarget.bed
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/cnvkit/baits.target.bed
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md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
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- path: output/cnvkit/reference.cnn
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md5sum: ac99c1ad8b917b96ae15119146c91ab9
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- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test.paired_end.sorted.bintest.cns
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md5sum: 6544d979475def8a9f69ba42a985668d
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- path: output/cnvkit/test.paired_end.sorted.call.cns
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md5sum: f2ca59b4d50b0c317adc526c1b99b622
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- path: output/cnvkit/test.paired_end.sorted.cnr
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md5sum: 7e37d73ab604dbc3fe4ebb56aca9bdc3
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- path: output/cnvkit/test.paired_end.sorted.cns
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md5sum: 060af1aa637ed51812af19bcce24fcfe
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- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
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md5sum: 3fe80b6013ffc3e9968345e810158215
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- path: output/cnvkit/test.single_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
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md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
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- name: cnvkit batch test_cnvkit_wgs
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command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c tests/config/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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files:
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- path: output/cnvkit/genome.antitarget.bed
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/cnvkit/genome.bed
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md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
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- path: output/cnvkit/genome.target.bed
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md5sum: a13353ae9c8405e701390c069255bbd2
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- path: output/cnvkit/reference.cnn
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md5sum: 05c6211e0179885b8a83e44fd21d5f86
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- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
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md5sum: ff526714696aa49bdc1dc8d00d965266
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- path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test2.paired_end.sorted.bintest.cns
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md5sum: 6544d979475def8a9f69ba42a985668d
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- path: output/cnvkit/test2.paired_end.sorted.call.cns
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md5sum: f6de754c34f780e6befee5b3ff0893f8
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- path: output/cnvkit/test2.paired_end.sorted.cnr
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md5sum: 80318d06c6b095945a0fb0e85e887cbc
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- path: output/cnvkit/test2.paired_end.sorted.cns
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md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
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- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
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md5sum: 6ae6b3fce7299eedca6133d911c38fe1
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- name: cnvkit batch test_cnvkit_cram
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command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_cram -c tests/config/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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files:
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- path: output/cnvkit/genome.antitarget.bed
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/cnvkit/genome.bed
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md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
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- path: output/cnvkit/genome.target.bed
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md5sum: a13353ae9c8405e701390c069255bbd2
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- path: output/cnvkit/reference.cnn
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md5sum: 05c6211e0179885b8a83e44fd21d5f86
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- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
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md5sum: ff526714696aa49bdc1dc8d00d965266
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- path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
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md5sum: 203caf8cef6935bb50b4138097955cb8
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- path: output/cnvkit/test2.paired_end.sorted.bintest.cns
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md5sum: 6544d979475def8a9f69ba42a985668d
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- path: output/cnvkit/test2.paired_end.sorted.call.cns
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md5sum: f6de754c34f780e6befee5b3ff0893f8
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- path: output/cnvkit/test2.paired_end.sorted.cnr
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md5sum: 80318d06c6b095945a0fb0e85e887cbc
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- path: output/cnvkit/test2.paired_end.sorted.cns
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md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
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- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
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md5sum: 6ae6b3fce7299eedca6133d911c38fe1
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- name: cnvkit batch test_cnvkit_tumoronly
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command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c tests/config/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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files:
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- path: output/cnvkit/reference.antitarget-tmp.bed
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/cnvkit/reference.target-tmp.bed
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md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
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