Merge branch 'master' into add_compression_to_bam2fq

This commit is contained in:
Lauri Mesilaakso 2022-05-03 11:13:55 +03:00 committed by GitHub
commit 773e6f8e93
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15 changed files with 167 additions and 0 deletions

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@ -43,4 +43,15 @@ process GATK4_MERGEBAMALIGNMENT {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
touch ${prefix}.vcf.gz.stats
touch ${prefix}.f1r2.tar.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -39,4 +39,15 @@ process GATK4_REVERTSAM {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.reverted.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -40,4 +40,17 @@ process GATK4_SAMTOFASTQ {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.fastq.gz
touch ${prefix}_1.fastq.gz
touch ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

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@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
touch ${prefix}.cram
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

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@ -14,3 +14,14 @@ workflow test_gatk4_mergebamalignment {
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
}
workflow test_gatk4_mergebamalignment_stubs {
input = [ [ id:'test' ], // meta map
"test_foo.bam",
"test_bar.bam"
]
fasta = "genome.fasta"
dict = "genome.fasta.dict"
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
}

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@ -7,3 +7,12 @@
- path: output/gatk4/test.bam
md5sum: e6f1b343700b7ccb94e81ae127433988
- path: output/gatk4/versions.yml
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
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
tags:
- gatk4
- gatk4/mergebamalignment
files:
- path: output/gatk4/test.bam
- path: output/gatk4/versions.yml

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@ -118,3 +118,25 @@ workflow test_gatk4_mutect2_mitochondria {
GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
}
workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
[ "foo_paired.bam",
"foo_paired2.bam"
],
[ "foo_paired.bam.bai",
"foo_paired2.bam.bai"
],
[]
]
fasta = "genome.fasta"
fai = "genome.fasta.fai"
dict = "genome.fasta.dict"
germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
}

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@ -69,3 +69,15 @@
md5sum: fc6ea14ca2da346babe78161beea28c9
- path: output/gatk4/test.vcf.gz.tbi
- path: output/gatk4/versions.yml
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
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
tags:
- gatk4
- gatk4/mutect2
files:
- path: output/gatk4/test.f1r2.tar.gz
- path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.stats
- path: output/gatk4/test.vcf.gz.tbi
- path: output/gatk4/versions.yml

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@ -11,3 +11,11 @@ workflow test_gatk4_revertsam {
GATK4_REVERTSAM ( input )
}
workflow test_gatk4_revertsam_stubs {
input = [ [ id:'test' ], // meta map
"foo_paired_end.bam"
]
GATK4_REVERTSAM ( input )
}

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@ -7,3 +7,12 @@
- path: output/gatk4/test.reverted.bam
md5sum: f783a88deb45c3a2c20ca12cbe1c5652
- path: output/gatk4/versions.yml
- name: gatk4 revertsam test_gatk4_revertsam_stubs
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
tags:
- gatk4
- gatk4/revertsam
files:
- path: output/gatk4/test.reverted.bam
- path: output/gatk4/versions.yml

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@ -19,3 +19,11 @@ workflow test_gatk4_samtofastq_paired_end {
GATK4_SAMTOFASTQ ( input )
}
workflow test_gatk4_samtofastq_paired_end_stubs {
input = [ [ id:'test', single_end: false ], // meta map
[ "foo_paired_end.bam" ]
]
GATK4_SAMTOFASTQ ( input )
}

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@ -19,3 +19,13 @@
- path: output/gatk4/test_2.fastq.gz
md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
- path: output/gatk4/versions.yml
- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
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
tags:
- gatk4
- gatk4/samtofastq
files:
- path: output/gatk4/test_1.fastq.gz
- path: output/gatk4/test_2.fastq.gz
- path: output/gatk4/versions.yml

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@ -22,3 +22,12 @@ workflow test_samtools_view_cram {
SAMTOOLS_VIEW ( input, fasta )
}
workflow test_samtools_view_stubs {
input = [ [ id:'test', single_end:false ], // meta map
"foo_paired_end.bam",
[]
]
SAMTOOLS_VIEW ( input, [] )
}

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@ -14,3 +14,11 @@
- samtools
files:
- path: output/samtools/test.cram
- name: samtools view test_samtools_view_stubs
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
tags:
- samtools/view
- samtools
files:
- path: output/samtools/test.bam