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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 19:25:40 -04:00
- name: gatk4 markduplicates test_gatk4_markduplicates
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
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 19:25:40 -04:00
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 11:10:49 -05:00
- 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 07:01:05 -04:00
files:
- path: output/gatk4/test.bai
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
md5sum: 4ac375b5288501c832bc3e4773f06d39
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 07:01:05 -04:00
- path: output/gatk4/test.bam
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
md5sum: c1a0d25c5f65514e72aa490326557a88
- path: output/gatk4/test.bam.metrics
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 07:01:05 -04:00
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
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 07:01:05 -04:00
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 11:10:49 -05:00
- 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 19:25:40 -04:00
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 07:01:05 -04:00
- path: output/gatk4/test.bai
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
md5sum: 832fbc6b3c3266d024fc7131ffd1b45d
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 19:25:40 -04:00
- path: output/gatk4/test.bam
MD finally supports cram output (#2019) * MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 05:04:58 -04:00
md5sum: 36909e80bde1aa547fae6382fd35764d
- path: output/gatk4/test.bam.metrics
contains:
- "testN"
- "2820"
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_cram_output
command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_cram_output -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
tags:
- gatk4
- gatk4/markduplicates
files:
- path: output/gatk4/test.cram
- path: output/gatk4/test.cram.crai
md5sum: 53a329f0828210e317ad81b0e6ca4bc5
- path: output/gatk4/test.cram.metrics
contains:
- "testN"
- "2820"
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