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nf-core_modules/tests/modules/cnvkit/batch/test.yml

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added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_hybrid_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
tags:
- cnvkit
added test & corrected cram input
2022-05-20 07:13:27 +00:00
- cnvkit/batch
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
files:
- path: output/cnvkit/baits.antitarget.bed
- path: output/cnvkit/baits.target.bed
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
- path: output/cnvkit/reference.cnn
added test & corrected cram input
2022-05-20 07:13:27 +00:00
md5sum: 035d031f54c5f1b43b903da96559b475
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.bintest.cns
md5sum: 6544d979475def8a9f69ba42a985668d
- path: output/cnvkit/test.paired_end.sorted.call.cns
md5sum: f2ca59b4d50b0c317adc526c1b99b622
- path: output/cnvkit/test.paired_end.sorted.cnr
md5sum: 7e37d73ab604dbc3fe4ebb56aca9bdc3
- path: output/cnvkit/test.paired_end.sorted.cns
md5sum: 060af1aa637ed51812af19bcce24fcfe
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
md5sum: 3fe80b6013ffc3e9968345e810158215
- path: output/cnvkit/test.single_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_wgs_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
tags:
- cnvkit
added test & corrected cram input
2022-05-20 07:13:27 +00:00
- cnvkit/batch
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
files:
- path: output/cnvkit/genome.antitarget.bed
- path: output/cnvkit/genome.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: output/cnvkit/genome.target.bed
md5sum: a13353ae9c8405e701390c069255bbd2
- path: output/cnvkit/reference.cnn
added test & corrected cram input
2022-05-20 07:13:27 +00:00
md5sum: 1606a85410bfaa79464be6e98699aa83
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
md5sum: ff526714696aa49bdc1dc8d00d965266
- path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test2.paired_end.sorted.bintest.cns
md5sum: 6544d979475def8a9f69ba42a985668d
- path: output/cnvkit/test2.paired_end.sorted.call.cns
md5sum: f6de754c34f780e6befee5b3ff0893f8
- path: output/cnvkit/test2.paired_end.sorted.cnr
md5sum: 80318d06c6b095945a0fb0e85e887cbc
- path: output/cnvkit/test2.paired_end.sorted.cns
md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_cram_wgs_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
tags:
- cnvkit
added test & corrected cram input
2022-05-20 07:13:27 +00:00
- cnvkit/batch
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
files:
- path: output/cnvkit/genome.antitarget.bed
- path: output/cnvkit/genome.bed
md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
- path: output/cnvkit/genome.target.bed
md5sum: a13353ae9c8405e701390c069255bbd2
- path: output/cnvkit/reference.cnn
added test & corrected cram input
2022-05-20 07:13:27 +00:00
md5sum: 1606a85410bfaa79464be6e98699aa83
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
md5sum: ff526714696aa49bdc1dc8d00d965266
- path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test2.paired_end.sorted.bintest.cns
md5sum: 6544d979475def8a9f69ba42a985668d
- path: output/cnvkit/test2.paired_end.sorted.call.cns
md5sum: f6de754c34f780e6befee5b3ff0893f8
- path: output/cnvkit/test2.paired_end.sorted.cnr
md5sum: 80318d06c6b095945a0fb0e85e887cbc
- path: output/cnvkit/test2.paired_end.sorted.cns
md5sum: 76afa47afc4bd5de35aee8fdb54d3d3a
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
tags:
added test & corrected cram input
2022-05-20 07:13:27 +00:00
- cnvkit
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
- cnvkit/batch
added test & corrected cram input
2022-05-20 07:13:27 +00:00
files:
adjust cnvkit/batch for germline mode
2022-06-01 15:35:02 +00:00
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/reference_chr21.target-tmp.bed
md5sum: 657b25dbda8516624efa8cb2cf3716ca
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: f7caeca04aba28b125ce26b511f42afb
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: d9bdb71ce807051369577ee7f807a40c
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 2b56aac606ba6183d018b30ca58afcec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
added test & corrected cram input
2022-05-20 07:13:27 +00:00
added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
added test & corrected cram input
2022-05-20 07:13:27 +00:00
tags:
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
- cnvkit
added test & corrected cram input
2022-05-20 07:13:27 +00:00
- cnvkit/batch
CNVkit: Make targets file optional when running in WGS mode (#1030) * 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>
2021-11-21 19:56:57 +00:00
files:
adjust cnvkit/batch for germline mode
2022-06-01 15:35:02 +00:00
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/reference_chr21.target-tmp.bed
md5sum: 657b25dbda8516624efa8cb2cf3716ca
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: f7caeca04aba28b125ce26b511f42afb
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: d9bdb71ce807051369577ee7f807a40c
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 2b56aac606ba6183d018b30ca58afcec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
added fasta_fai as input + changed if statements
2022-06-02 10:57:50 +00:00
- name: cnvkit batch test_cnvkit_germline_hybrid_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/multi_intervals.antitarget.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/multi_intervals.target.bed
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
- path: output/cnvkit/reference.cnn
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: 68b62b75cd91b2ffe5633686fb943490
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: df196edd72613c59186f4d87df3dc4a4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: 3b4fc0cc73be78f978cfe2422470753e
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
- name: cnvkit batch test_cnvkit_germline_hybrid_bam
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
adjust cnvkit/batch for germline mode
2022-06-01 15:35:02 +00:00
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/multi_intervals.antitarget.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/multi_intervals.target.bed
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
- path: output/cnvkit/reference.cnn
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: 68b62b75cd91b2ffe5633686fb943490
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: df196edd72613c59186f4d87df3dc4a4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: 3b4fc0cc73be78f978cfe2422470753e
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
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