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Update stubs for samtools idxstats #3665

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merged 4 commits into from
Jul 25, 2023
Merged

Update stubs for samtools idxstats #3665

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1730700
Update stubs
Jul 20, 2023
baf9f62
Update stubs for samtools idxstats
Jul 20, 2023
bb58a0f
Merge branch 'master' into idxstats
ramsainanduri Jul 24, 2023
80fb369
Merge branch 'master' into idxstats
ramsainanduri Jul 25, 2023
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12 changes: 12 additions & 0 deletions modules/nf-core/samtools/idxstats/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.idxstats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
15 changes: 12 additions & 3 deletions tests/modules/nf-core/samtools/idxstats/main.nf
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Expand Up @@ -6,9 +6,18 @@ include { SAMTOOLS_IDXSTATS } from '../../../../../modules/nf-core/samtools/idxs

workflow test_samtools_idxstats {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]

SAMTOOLS_IDXSTATS ( input )
}

workflow test_samtools_idxstats_stub {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]

SAMTOOLS_IDXSTATS ( input )
}
9 changes: 9 additions & 0 deletions tests/modules/nf-core/samtools/idxstats/test.yml
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Expand Up @@ -7,3 +7,12 @@
- path: output/samtools/test.idxstats
md5sum: df60a8c8d6621100d05178c93fb053a2
- path: output/samtools/versions.yml

- name: samtools idxstats test_samtools_idxstats_stub
command: nextflow run ./tests/modules/nf-core/samtools/idxstats -entry test_samtools_idxstats_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/idxstats/nextflow.config -stub
tags:
- samtools/idxstats
- samtools
files:
- path: output/samtools/test.idxstats
- path: output/samtools/versions.yml
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