mirror of
https://github.com/MillironX/nf-core_modules.git
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ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
26 lines
905 B
YAML
26 lines
905 B
YAML
- name: gatk4 applybqsr test_gatk4_applybqsr
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command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
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tags:
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- gatk4/applybqsr
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- gatk4
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files:
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- path: output/gatk4/test.bam
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md5sum: 87a2eabae2b7b41574f966612b5addae
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- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
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command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
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tags:
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- gatk4/applybqsr
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- gatk4
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files:
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- path: output/gatk4/test.bam
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md5sum: 9c015d3c1dbd9eee793b7386f432b6aa
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- name: gatk4 applybqsr test_gatk4_applybqsr_cram
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command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config
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tags:
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- gatk4/applybqsr
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- gatk4
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files:
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- path: output/gatk4/test.bam
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md5sum: 02f84815fdbc99c21c8d42ebdcabbbf7
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