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nf-core_modules/tests/modules/gatk4/markduplicates/test.yml

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gatk4 markduplicates (#356) * new module gatk4/markduplicates * add tests * add gatk4_markduplicates entry in pytest_software.yml * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Fix EC lint * Update md5sum Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
- name: gatk4 markduplicates test_gatk4_markduplicates
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
gatk4 markduplicates (#356) * new module gatk4/markduplicates * add tests * add gatk4_markduplicates entry in pytest_software.yml * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Fix EC lint * Update md5sum Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
tags:
- gatk4
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
- gatk4/markduplicates
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
files:
- path: output/gatk4/test.bai
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: c8f7a9e426c768577f88f59cb1336bf3
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
- path: output/gatk4/test.bam
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: fba0c99a0b087c90113a210e4465f91b
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
- path: output/gatk4/test.metrics
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
- path: output/gatk4/versions.yml
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: dacbab0e112d2403b09df138d4e62895
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
tags:
- gatk4
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
- gatk4/markduplicates
gatk4 markduplicates (#356) * new module gatk4/markduplicates * add tests * add gatk4_markduplicates entry in pytest_software.yml * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Fix EC lint * Update md5sum Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
files:
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
- path: output/gatk4/test.bai
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: 325932c51f6898b02dfec469c984ba28
gatk4 markduplicates (#356) * new module gatk4/markduplicates * add tests * add gatk4_markduplicates entry in pytest_software.yml * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Fix EC lint * Update md5sum Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
- path: output/gatk4/test.bam
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: f7cba8104e3a7024a5e00c02304f7dea
Update to allow cram + update needed to use the gatk4 modules in sarek (#976) * 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>
2021-10-29 11:01:05 +00:00
- path: output/gatk4/test.metrics
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
- path: output/gatk4/versions.yml
Log4j again (#1202) * Log4j again * Update checksums
2022-01-12 12:55:54 +00:00
md5sum: 14d0d085df7d2f9e770578d92c329299
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