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test_gatk4spark.yml
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- name: Run default pipeline with gatk4spark
command: nextflow run main.nf -profile test,use_gatk_spark,spark --outdir results
tags:
- gatk4spark
- preprocessing
files:
- path: results/csv/markduplicates.csv
md5sum: 0dec46c4dc83acc263efc234805e9349
- path: results/csv/markduplicates_no_table.csv
md5sum: f274df0cba98b2641fdc2a9becb23f78
- path: results/csv/recalibrated.csv
md5sum: f6ab55df6c87f44c2d8651a2be0b959f
- path: results/multiqc
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary file changes md5sums on reruns
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary file changes md5sums on reruns
- path: results/reports/fastqc/test2-test_L1
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
# text-based file changes md5sums on reruns
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
should_exist: false
- name: Run default pipeline with gatk4spark and skipping all QC steps
command: nextflow run main.nf -profile test,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
tags:
- gatk4spark
- preprocessing
- skip_qc
files:
- path: results/csv/markduplicates.csv
md5sum: 0dec46c4dc83acc263efc234805e9349
- path: results/csv/markduplicates_no_table.csv
md5sum: f274df0cba98b2641fdc2a9becb23f78
- path: results/csv/recalibrated.csv
md5sum: f6ab55df6c87f44c2d8651a2be0b959f
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary file changes md5sums on reruns
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary file changes md5sums on reruns
- path: results/multiqc
should_exist: false
- path: results/reports/fastqc
should_exist: false
- path: results/reports/markduplicates
should_exist: false
- path: results/reports/mosdepth
should_exist: false
- path: results/reports/samtools
should_exist: false
- name: Run save_output_as_bam with gatk4 spark
command: nextflow run main.nf -profile test,use_gatk_spark,spark --save_output_as_bam --outdir results
tags:
- gatk4spark
- preprocessing
- save_output_as_bam
files:
- path: results/csv/markduplicates.csv
md5sum: 974a2375ca62c56078076e40768b6367
- path: results/csv/markduplicates_no_table.csv
md5sum: d508740377e048822c9e2f11f048a56d
- path: results/csv/recalibrated.csv
md5sum: e5f9c71eb6746324a68a0ef989c50a28
- path: results/multiqc
- path: results/preprocessing/markduplicates/test2/test2.md.bam
# conda changes md5sums for test
- path: results/preprocessing/markduplicates/test2/test2.md.bam.bai
# conda changes md5sums for test
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.bam
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.bam.bai
# binary changes md5sums on reruns
- path: results/reports/fastqc/test2-test_L1
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
# text-based file changes md5sums on reruns
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test