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Merge pull request #1623 from nf-core/correcting_stubs
fix added correct entry workflow in test.yml
This commit is contained in:
Lucpen
GitHub
commit
38d4f81d20
10 changed files with 25 additions and 25 deletions
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@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
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workflow test_gatk4_mergebamalignment_stubs {
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input = [ [ id:'test' ], // meta map
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"test_foo.bam",
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"test_bar.bam"
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
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]
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fasta = "genome.fasta"
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dict = "genome.fasta.dict"
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
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}
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@ -9,7 +9,7 @@
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- path: output/gatk4/versions.yml
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- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
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command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
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command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/mergebamalignment
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@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
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}
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workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
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input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
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[ "foo_paired.bam",
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"foo_paired2.bam"
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input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
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],
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[ "foo_paired.bam.bai",
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"foo_paired2.bam.bai"
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
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],
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[]
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]
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fasta = "genome.fasta"
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fai = "genome.fasta.fai"
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dict = "genome.fasta.dict"
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germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
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germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
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panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
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panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
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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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germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
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germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
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panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
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panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
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GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
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}
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@ -71,7 +71,7 @@
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- path: output/gatk4/versions.yml
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- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
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command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/mutect2
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@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
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workflow test_gatk4_revertsam_stubs {
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input = [ [ id:'test' ], // meta map
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"foo_paired_end.bam"
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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GATK4_REVERTSAM ( input )
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@ -9,7 +9,7 @@
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- path: output/gatk4/versions.yml
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- name: gatk4 revertsam test_gatk4_revertsam_stubs
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command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
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command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/revertsam
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@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
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}
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workflow test_gatk4_samtofastq_paired_end_stubs {
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input = [ [ id:'test', single_end: false ], // meta map
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[ "foo_paired_end.bam" ]
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input = [ [ id:'test', single_end: true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
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]
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GATK4_SAMTOFASTQ ( input )
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@ -21,7 +21,7 @@
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- path: output/gatk4/versions.yml
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- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
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command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
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command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
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tags:
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- gatk4
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- gatk4/samtofastq
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@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
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workflow test_samtools_view_stubs {
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input = [ [ id:'test', single_end:false ], // meta map
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"foo_paired_end.bam",
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
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[]
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]
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@ -16,7 +16,7 @@
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- path: output/samtools/test.cram
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- name: samtools view test_samtools_view_stubs
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command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
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command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
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tags:
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- samtools/view
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- samtools
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