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added test & corrected cram input
This commit is contained in:
SusiJo
parent
5a1297cc7d
commit
3d57caa683
2 changed files with 38 additions and 14 deletions
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@ -35,8 +35,8 @@ workflow test_cnvkit_cram {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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@ -53,5 +53,18 @@ workflow test_cnvkit_tumoronly {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, [], [], reference )
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CNVKIT_TUMORONLY ( input, fasta, [], reference )
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}
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workflow test_cnvkit_tumoronly_cram {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, fasta, [], reference )
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}
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@ -1,15 +1,15 @@
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- 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 -c ./tests/modules/cnvkit/batch/nextflow.config
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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- cnvkit/batch
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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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md5sum: 035d031f54c5f1b43b903da96559b475
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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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@ -28,10 +28,10 @@
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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 -c ./tests/modules/cnvkit/batch/nextflow.config
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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- cnvkit/batch
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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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@ -40,7 +40,7 @@
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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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md5sum: 1606a85410bfaa79464be6e98699aa83
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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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@ -59,10 +59,10 @@
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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 -c ./tests/modules/cnvkit/batch/nextflow.config
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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- cnvkit/batch
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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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@ -71,7 +71,7 @@
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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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md5sum: 1606a85410bfaa79464be6e98699aa83
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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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@ -90,10 +90,21 @@
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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 -c ./tests/modules/cnvkit/batch/nextflow.config
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit/batch
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- cnvkit
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- cnvkit/batch
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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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- name: cnvkit batch test_cnvkit_tumoronly_cram
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit
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- cnvkit/batch
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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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