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Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621)
* feat added stubs to picard_liftovervcf * feat adding stubs to gatk4_mergevcfs * feat adding stubs to gatk4_filtermutectcalls * fix tests * fix output name filtermutectcalls * fix test * fix added missing [ * Update tests/modules/gatk4/mergevcfs/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/gatk4/filtermutectcalls/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/picard/liftovervcf/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Trying something on picard_liftovervcf * fix adding test data for stubs * fix added bracket and unindented workflow * fix picard 2.27.1 -> 2.27.0 to solve PaddingError * Update main.nf fix added tbi to stub Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
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9 changed files with 109 additions and 1 deletions
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@ -54,4 +54,17 @@ process GATK4_FILTERMUTECTCALLS {
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.vcf.gz
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touch ${prefix}.vcf.gz.tbi
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touch ${prefix}.vcf.gz.filteringStats.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -44,4 +44,16 @@ process GATK4_MERGEVCFS {
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.vcf.gz
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touch ${prefix}.vcf.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -43,7 +43,19 @@ process PICARD_LIFTOVERVCF {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
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picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.lifted.vcf.gz
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touch ${prefix}.unlifted.vcf.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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@ -63,3 +63,23 @@ workflow test_gatk4_filtermutectcalls_use_val {
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GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
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}
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workflow test_gatk4_filtermutectcalls_base_stubs {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
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[],
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[],
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[],
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict )
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}
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@ -33,3 +33,14 @@
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md5sum: 95cc3e37705bd3b97a292c5d46ab82f3
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base_stubs
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command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/filtermutectcalls
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files:
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- path: output/gatk4/test.filtered.vcf.gz
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- path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
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- path: output/gatk4/test.filtered.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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@ -24,3 +24,12 @@ workflow test_gatk4_mergevcfs_no_dict {
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GATK4_MERGEVCFS ( input, [] )
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}
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workflow test_gatk4_mergevcfs_no_dict_stubs {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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GATK4_MERGEVCFS ( input, [] )
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}
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@ -19,3 +19,12 @@
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- path: output/gatk4/test.vcf.gz
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md5sum: 5b289bda88d3a3504f2e19ee8cff177c
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- path: output/gatk4/versions.yml
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- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict_stubs
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command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_no_dict_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config -stub-run
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tags:
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- gatk4/mergevcfs
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- gatk4
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/versions.yml
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@ -15,3 +15,15 @@ workflow test_picard_liftovervcf {
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PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
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}
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workflow test_picard_liftovervcf_stubs {
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input_vcf = [ [ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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chain = file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
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}
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@ -9,3 +9,13 @@
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- "chr22"
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- path: output/picard/test.unlifted.vcf.gz
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- path: output/picard/versions.yml
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- name: picard liftovervcf test_picard_liftovervcf_stubs
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command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c tests/config/nextflow.config -stub-run
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tags:
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- picard/liftovervcf
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- picard
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files:
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- path: output/picard/test.lifted.vcf.gz
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- path: output/picard/test.unlifted.vcf.gz
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- path: output/picard/versions.yml
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