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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>
23 lines
899 B
YAML
23 lines
899 B
YAML
- name: gatk4 markduplicates test_gatk4_markduplicates
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command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config
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tags:
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- gatk4/markduplicates
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- gatk4
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files:
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- path: output/gatk4/test.bai
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md5sum: e9c125e82553209933883b4fe2b8d7c2
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- path: output/gatk4/test.bam
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md5sum: bda9a7bf5057f2288ed70be3eb8a753f
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- path: output/gatk4/test.metrics
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- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
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command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config
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tags:
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- gatk4/markduplicates
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- gatk4
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files:
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- path: output/gatk4/test.bai
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md5sum: 93cebe29e7cca2064262b739235cca9b
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- path: output/gatk4/test.bam
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md5sum: dcd6f584006b04141fb787001a8ecacc
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- path: output/gatk4/test.metrics
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