From 3d57caa683a48a014abf986cfdaaf0b9f6ff9676 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Fri, 20 May 2022 09:13:27 +0200 Subject: [PATCH] added test & corrected cram input --- tests/modules/cnvkit/batch/main.nf | 19 ++++++++++++++--- tests/modules/cnvkit/batch/test.yml | 33 +++++++++++++++++++---------- 2 files changed, 38 insertions(+), 14 deletions(-) diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf index 6b40dec6..15b5dfe6 100755 --- a/tests/modules/cnvkit/batch/main.nf +++ b/tests/modules/cnvkit/batch/main.nf @@ -35,8 +35,8 @@ workflow test_cnvkit_cram { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) @@ -53,5 +53,18 @@ workflow test_cnvkit_tumoronly { fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true) - CNVKIT_TUMORONLY ( input, [], [], reference ) + CNVKIT_TUMORONLY ( input, fasta, [], reference ) +} + +workflow test_cnvkit_tumoronly_cram { + + input = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true) + + CNVKIT_TUMORONLY ( input, fasta, [], reference ) } diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml index 57af3603..9bce265a 100755 --- a/tests/modules/cnvkit/batch/test.yml +++ b/tests/modules/cnvkit/batch/test.yml @@ -1,15 +1,15 @@ - name: cnvkit batch test_cnvkit_hybrid - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config tags: - - cnvkit/batch - cnvkit + - cnvkit/batch files: - path: output/cnvkit/baits.antitarget.bed md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/cnvkit/baits.target.bed md5sum: 26d25ff2d6c45b6d92169b3559c6acdb - path: output/cnvkit/reference.cnn - md5sum: ac99c1ad8b917b96ae15119146c91ab9 + md5sum: 035d031f54c5f1b43b903da96559b475 - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test.paired_end.sorted.bintest.cns @@ -28,10 +28,10 @@ md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7 - name: cnvkit batch test_cnvkit_wgs - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config tags: - - cnvkit/batch - cnvkit + - cnvkit/batch files: - path: output/cnvkit/genome.antitarget.bed md5sum: d41d8cd98f00b204e9800998ecf8427e @@ -40,7 +40,7 @@ - path: output/cnvkit/genome.target.bed md5sum: a13353ae9c8405e701390c069255bbd2 - path: output/cnvkit/reference.cnn - md5sum: 05c6211e0179885b8a83e44fd21d5f86 + md5sum: 1606a85410bfaa79464be6e98699aa83 - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn @@ -59,10 +59,10 @@ md5sum: 6ae6b3fce7299eedca6133d911c38fe1 - name: cnvkit batch test_cnvkit_cram - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config tags: - - cnvkit/batch - cnvkit + - cnvkit/batch files: - path: output/cnvkit/genome.antitarget.bed md5sum: d41d8cd98f00b204e9800998ecf8427e @@ -71,7 +71,7 @@ - path: output/cnvkit/genome.target.bed md5sum: a13353ae9c8405e701390c069255bbd2 - path: output/cnvkit/reference.cnn - md5sum: 05c6211e0179885b8a83e44fd21d5f86 + md5sum: 1606a85410bfaa79464be6e98699aa83 - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn @@ -90,10 +90,21 @@ md5sum: 6ae6b3fce7299eedca6133d911c38fe1 - name: cnvkit batch test_cnvkit_tumoronly - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config tags: - - cnvkit/batch - cnvkit + - cnvkit/batch + files: + - path: output/cnvkit/reference.antitarget-tmp.bed + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/cnvkit/reference.target-tmp.bed + md5sum: 26d25ff2d6c45b6d92169b3559c6acdb + +- name: cnvkit batch test_cnvkit_tumoronly_cram + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config + tags: + - cnvkit + - cnvkit/batch files: - path: output/cnvkit/reference.antitarget-tmp.bed md5sum: d41d8cd98f00b204e9800998ecf8427e