From f6953b51478d24a4caf84b40d92bba3350a38507 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 1 Jun 2022 17:35:02 +0200 Subject: [PATCH 1/3] adjust cnvkit/batch for germline mode --- modules/cnvkit/batch/main.nf | 38 +++++++++++------ tests/config/test_data.config | 6 +-- tests/modules/cnvkit/batch/main.nf | 22 ++++++++-- tests/modules/cnvkit/batch/test.yml | 63 ++++++++++++++++++++++++++--- 4 files changed, 104 insertions(+), 25 deletions(-) diff --git a/modules/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf index c1f9ef87..b467c6f2 100644 --- a/modules/cnvkit/batch/main.nf +++ b/modules/cnvkit/batch/main.nf @@ -28,34 +28,48 @@ process CNVKIT_BATCH { script: def args = task.ext.args ?: '' - // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow - // input pair is assumed to have same extension if both exist - def is_cram = tumor.Extension == "cram" ? true : false - def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}" + def tumor_exists = tumor ? true : false + def normal_exists = normal ? true : false + + // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow + def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false + def normal_cram = normal_exists && normal.Extension == "cram" ? true : false + + def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}" - // do not run samtools on normal samples in tumor_only mode - def normal_exists = normal ? true: false // tumor_only mode does not need fasta & target // instead it requires a pre-computed reference.cnn which is built from fasta & target def (normal_out, normal_args, fasta_args) = ["", "", ""] if (normal_exists){ def normal_prefix = normal.BaseName - normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}" - normal_args = normal_prefix ? "--normal $normal_out" : "" + normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}" fasta_args = fasta ? "--fasta $fasta" : "" + + // germline mode + // normal samples must be input without a flag + // requires flag --normal to be empty + if(!tumor_exists){ + tumor_out = normal.BaseName + ".bam" + normal_args = "--normal " + } + // somatic mode + else { + normal_args = normal_prefix ? "--normal $normal_out" : "" + } } def target_args = targets ? "--targets $targets" : "" def reference_args = reference ? "--reference $reference" : "" """ - if $is_cram; then + if $tumor_cram; then samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out - if $normal_exists; then - samtools view -T $fasta $normal -@ $task.cpus -o $normal_out - fi fi + if $normal_cram; then + samtools view -T $fasta $normal -@ $task.cpus -o $normal_out + fi + cnvkit.py \\ batch \\ diff --git a/tests/config/test_data.config b/tests/config/test_data.config index cf7d45f6..bef6f0c9 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -23,6 +23,8 @@ params { test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12" baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed" + reference_cnn = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn" + kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2" kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz" @@ -145,6 +147,7 @@ params { genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + genome_21_reference_cnn = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" dbsnp_146_hg38_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" @@ -414,9 +417,6 @@ params { 'txt' { hello = "${test_data_dir}/generic/txt/hello.txt" } - 'cnn' { - reference = "${test_data_dir}/generic/cnn/reference.cnn" - } 'cooler'{ test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf index 988ed3ad..c93e3a00 100755 --- a/tests/modules/cnvkit/batch/main.nf +++ b/tests/modules/cnvkit/batch/main.nf @@ -5,6 +5,7 @@ nextflow.enable.dsl = 2 include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf' include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf' include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' +include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf' workflow test_cnvkit_hybrid { @@ -47,10 +48,10 @@ workflow test_cnvkit_tumoronly { 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']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), [] ] - reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true) + reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true) CNVKIT_TUMORONLY ( input, [], [], reference ) } @@ -59,11 +60,24 @@ workflow test_cnvkit_tumoronly_cram { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_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) + reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true) CNVKIT_TUMORONLY ( input, fasta, [], reference ) } + +workflow test_cnvkit_germline_cram { + + input = [ + [ id:'test'], // meta map + [], + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + + CNVKIT_GERMLINE ( input, fasta, targets, []) +} diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml index 00d6a767..928a08de 100755 --- a/tests/modules/cnvkit/batch/test.yml +++ b/tests/modules/cnvkit/batch/test.yml @@ -92,9 +92,22 @@ - cnvkit - cnvkit/batch files: - - path: output/cnvkit/reference.antitarget-tmp.bed - - path: output/cnvkit/reference.target-tmp.bed - md5sum: 26d25ff2d6c45b6d92169b3559c6acdb + - 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 - 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 @@ -102,6 +115,44 @@ - cnvkit - cnvkit/batch files: - - path: output/cnvkit/reference.antitarget-tmp.bed - - path: output/cnvkit/reference.target-tmp.bed - md5sum: 26d25ff2d6c45b6d92169b3559c6acdb + - 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 + +- name: cnvkit batch test_cnvkit_germline_cram + command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_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 From 51be617b1ca9bff973655eb899d591ed6ab253b5 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 2 Jun 2022 11:09:55 +0200 Subject: [PATCH 2/3] fix untar output dir --- modules/untar/main.nf | 8 +++++++- tests/config/test_data.config | 2 ++ tests/modules/untar/main.nf | 10 ++++++++++ tests/modules/untar/test.yml | 12 ++++++++++-- 4 files changed, 29 insertions(+), 3 deletions(-) diff --git a/modules/untar/main.nf b/modules/untar/main.nf index 058d1764..29ab10a5 100644 --- a/modules/untar/main.nf +++ b/modules/untar/main.nf @@ -21,12 +21,18 @@ process UNTAR { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' untar = archive.toString() - '.tar.gz' + """ + mkdir output + tar \\ + -C output --strip-components 1 \\ -xzvf \\ $args \\ $archive \\ - $args2 \\ + $args2 + + mv output ${untar} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 39331664..4af77d92 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -323,6 +323,8 @@ params { test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor" + + test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" } 'pacbio' { primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta" diff --git a/tests/modules/untar/main.nf b/tests/modules/untar/main.nf index 9d6d4c6c..3b7daedd 100644 --- a/tests/modules/untar/main.nf +++ b/tests/modules/untar/main.nf @@ -12,3 +12,13 @@ workflow test_untar { UNTAR ( input ) } + + +workflow test_untar_different_output_path { + input = [ + [], + file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) + ] + + UNTAR ( input ) +} diff --git a/tests/modules/untar/test.yml b/tests/modules/untar/test.yml index 6d0d1d12..6599f105 100644 --- a/tests/modules/untar/test.yml +++ b/tests/modules/untar/test.yml @@ -1,5 +1,5 @@ -- name: untar - command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config +- name: untar test_untar + command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config tags: - untar files: @@ -9,3 +9,11 @@ md5sum: a033d00cf6759407010b21700938f543 - path: output/untar/kraken2/taxo.k2d md5sum: 094d5891cdccf2f1468088855c214b2c + +- name: untar test_untar_different_output_path + command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config + tags: + - untar + files: + - path: output/untar/flowcell/RunInfo.xml + md5sum: 03038959f4dd181c86bc97ae71fe270a From 2f3ddc90fbeda9fcf54f25b84465f5ac149d2b75 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Thu, 2 Jun 2022 12:57:50 +0200 Subject: [PATCH 3/3] added fasta_fai as input + changed if statements --- modules/cnvkit/batch/main.nf | 152 +++++++++++++++++++++++----- modules/cnvkit/batch/meta.yml | 4 + tests/modules/cnvkit/batch/main.nf | 44 +++++--- tests/modules/cnvkit/batch/test.yml | 49 ++++++--- 4 files changed, 200 insertions(+), 49 deletions(-) diff --git a/modules/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf index b467c6f2..090f7860 100644 --- a/modules/cnvkit/batch/main.nf +++ b/modules/cnvkit/batch/main.nf @@ -10,6 +10,7 @@ process CNVKIT_BATCH { input: tuple val(meta), path(tumor), path(normal) path fasta + path fasta_fai path targets path reference @@ -34,12 +35,15 @@ process CNVKIT_BATCH { // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false def normal_cram = normal_exists && normal.Extension == "cram" ? true : false + def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false + def normal_bam = normal_exists && normal.Extension == "bam" ? true : false def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}" // tumor_only mode does not need fasta & target // instead it requires a pre-computed reference.cnn which is built from fasta & target def (normal_out, normal_args, fasta_args) = ["", "", ""] + def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : "" if (normal_exists){ def normal_prefix = normal.BaseName @@ -48,9 +52,9 @@ process CNVKIT_BATCH { // germline mode // normal samples must be input without a flag - // requires flag --normal to be empty + // requires flag --normal to be empty [] if(!tumor_exists){ - tumor_out = normal.BaseName + ".bam" + tumor_out = "${normal_prefix}" + ".bam" normal_args = "--normal " } // somatic mode @@ -62,28 +66,130 @@ process CNVKIT_BATCH { def target_args = targets ? "--targets $targets" : "" def reference_args = reference ? "--reference $reference" : "" - """ - if $tumor_cram; then - samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out - fi - if $normal_cram; then - samtools view -T $fasta $normal -@ $task.cpus -o $normal_out - fi + // somatic_mode cram_input + if (tumor_cram && normal_cram){ + """ + samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out + samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args - cnvkit.py \\ - batch \\ - $tumor_out \\ - $normal_args \\ - $fasta_args \\ - $reference_args \\ - $target_args \\ - --processes $task.cpus \\ - $args + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } + // somatic_mode bam_input + else if (tumor_bam && normal_bam){ + """ + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } + // tumor_only_mode cram_input + else if(tumor_cram && !normal_exists){ + """ + samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out + + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } + // tumor_only bam_input + else if(tumor_bam && !normal_exists){ + """ + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } + // germline mode cram_input + // normal_args must be --normal [] + else if (normal_cram && !tumor_exists){ + """ + samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out + + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } + // germline mode bam_input + else if (normal_bam && !tumor_exists){ + """ + cnvkit.py \\ + batch \\ + $tumor_out \\ + $normal_args \\ + $fasta_args \\ + $reference_args \\ + $target_args \\ + --processes $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") + END_VERSIONS + """ + } - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") - END_VERSIONS - """ } diff --git a/modules/cnvkit/batch/meta.yml b/modules/cnvkit/batch/meta.yml index 2cd675c7..89762192 100644 --- a/modules/cnvkit/batch/meta.yml +++ b/modules/cnvkit/batch/meta.yml @@ -29,6 +29,10 @@ input: type: file description: | Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) + - fasta_fai: + type: file + description: | + Input reference genome fasta index (optional, but recommended for cram_input) - targetfile: type: file description: | diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf index c93e3a00..daf87a37 100755 --- a/tests/modules/cnvkit/batch/main.nf +++ b/tests/modules/cnvkit/batch/main.nf @@ -7,7 +7,7 @@ include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/ba include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf' -workflow test_cnvkit_hybrid { +workflow test_cnvkit_hybrid_somatic { input = [ [ id:'test' ], // meta map @@ -17,10 +17,10 @@ workflow test_cnvkit_hybrid { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true) - CNVKIT_HYBRID ( input, fasta, targets, [] ) + CNVKIT_HYBRID ( input, fasta, [], targets, [] ) } -workflow test_cnvkit_wgs { +workflow test_cnvkit_wgs_somatic { input = [ [ id:'test'], // meta map @@ -29,22 +29,24 @@ workflow test_cnvkit_wgs { ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - CNVKIT_WGS ( input, fasta, [], [] ) + CNVKIT_WGS ( input, fasta, [], [], [] ) } -workflow test_cnvkit_cram { +workflow test_cnvkit_cram_wgs_somatic { input = [ [ id:'test'], // meta map 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) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - CNVKIT_WGS ( input, fasta, [], [] ) + CNVKIT_WGS ( input, fasta, fasta_fai, [], [] ) } -workflow test_cnvkit_tumoronly { + +workflow test_cnvkit_tumoronly_hybrid_bam { input = [ [ id:'test'], // meta map @@ -53,10 +55,10 @@ workflow test_cnvkit_tumoronly { ] reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true) - CNVKIT_TUMORONLY ( input, [], [], reference ) + CNVKIT_TUMORONLY ( input, [], [], [], reference ) } -workflow test_cnvkit_tumoronly_cram { +workflow test_cnvkit_tumoronly_hybrid_cram { input = [ [ id:'test'], // meta map @@ -66,10 +68,10 @@ workflow test_cnvkit_tumoronly_cram { fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true) - CNVKIT_TUMORONLY ( input, fasta, [], reference ) + CNVKIT_TUMORONLY ( input, fasta, [], [], reference ) } -workflow test_cnvkit_germline_cram { +workflow test_cnvkit_germline_hybrid_cram { input = [ [ id:'test'], // meta map @@ -77,7 +79,21 @@ workflow test_cnvkit_germline_cram { file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true) ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) - CNVKIT_GERMLINE ( input, fasta, targets, []) + CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets, []) +} + +workflow test_cnvkit_germline_hybrid_bam { + + input = [ + [ id:'test'], // meta map + [], + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true) + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + + CNVKIT_GERMLINE ( input, fasta, [], targets, []) } diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml index 928a08de..006e142f 100755 --- a/tests/modules/cnvkit/batch/test.yml +++ b/tests/modules/cnvkit/batch/test.yml @@ -1,5 +1,5 @@ -- 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 +- 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 tags: - cnvkit - cnvkit/batch @@ -26,8 +26,8 @@ - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn 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 +- 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 tags: - cnvkit - cnvkit/batch @@ -56,8 +56,8 @@ - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn 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 +- 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 tags: - cnvkit - cnvkit/batch @@ -86,8 +86,8 @@ - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn 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 +- 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 tags: - cnvkit - cnvkit/batch @@ -109,8 +109,8 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 -- 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 +- 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 tags: - cnvkit - cnvkit/batch @@ -132,8 +132,33 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 -- name: cnvkit batch test_cnvkit_germline_cram - command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config +- 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 tags: - cnvkit - cnvkit/batch