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FIX: gatk4_spark checksum #1229

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Merged
FriederikeHanssen merged 2 commits into from
Sep 13, 2023
Merged

FIX: gatk4_spark checksum #1229

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b3c161a
update CHANGELOG
maxulysse Sep 13, 2023
5653213
update md5sums
maxulysse Sep 13, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1224](https://github.com/nf-core/sarek/pull/1224) - Update BCFTOOLS_SORT module with `--temp-dir .` added as option, which was required for Singularity
- [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests
- [#1227](https://github.com/nf-core/sarek/pull/1227) - Lint warning fix
- [#1229](https://github.com/nf-core/sarek/pull/1229) - Fix md5sum for gatk4_spark tests

### Dependencies

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140 changes: 70 additions & 70 deletions tests/test_gatk4_spark.yml
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Expand Up @@ -5,46 +5,46 @@
- preprocessing
files:
- path: results/csv/markduplicates.csv
md5sum: 0d6120bb99e92f6810343270711ca53e
md5sum: 0dec46c4dc83acc263efc234805e9349
- path: results/csv/markduplicates_no_table.csv
md5sum: 2a2d3d4842befd4def39156463859ee3
md5sum: f274df0cba98b2641fdc2a9becb23f78
- path: results/csv/recalibrated.csv
md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
md5sum: f6ab55df6c87f44c2d8651a2be0b959f
- path: results/multiqc
- path: results/preprocessing/markduplicates/test/test.md.cram
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary file changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary file changes md5sums on reruns
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
- 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/test/test.md.mosdepth.global.dist.txt
md5sum: 9269e959d5eec5273307693c6274f53e
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
md5sum: deb2df4f3ca19f441f0a22f04dea8723
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
md5sum: 96acf3439477a1448b7e1b43c020c7d0
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
md5sum: c259a9fd73f576626c3a29841c2dc019
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
md5sum: cf85ba4692f016af70db2a594d9effdf
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
md5sum: 9269e959d5eec5273307693c6274f53e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
md5sum: deb2df4f3ca19f441f0a22f04dea8723
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
md5sum: 96acf3439477a1448b7e1b43c020c7d0
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
md5sum: c259a9fd73f576626c3a29841c2dc019
- path: results/reports/samtools/test/test.md.cram.stats
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test
- path: results/preprocessing/mapped/
should_exist: false
Expand All @@ -56,20 +56,20 @@
- skip_qc
files:
- path: results/csv/markduplicates.csv
md5sum: 0d6120bb99e92f6810343270711ca53e
md5sum: 0dec46c4dc83acc263efc234805e9349
- path: results/csv/markduplicates_no_table.csv
md5sum: 2a2d3d4842befd4def39156463859ee3
md5sum: f274df0cba98b2641fdc2a9becb23f78
- path: results/csv/recalibrated.csv
md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
- path: results/preprocessing/markduplicates/test/test.md.cram
md5sum: f6ab55df6c87f44c2d8651a2be0b959f
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary file changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary file changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary file changes md5sums on reruns
- path: results/multiqc
should_exist: false
Expand All @@ -89,46 +89,46 @@
- save_output_as_bam
files:
- path: results/csv/markduplicates.csv
md5sum: 6004ab16b63012e336f6251396a983c5
md5sum: 974a2375ca62c56078076e40768b6367
- path: results/csv/markduplicates_no_table.csv
md5sum: 8a145eca178cfd02403d60122b9d3960
md5sum: d508740377e048822c9e2f11f048a56d
- path: results/csv/recalibrated.csv
md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
md5sum: e5f9c71eb6746324a68a0ef989c50a28
- path: results/multiqc
- path: results/preprocessing/markduplicates/test/test.md.bam
- path: results/preprocessing/markduplicates/test2/test2.md.bam
# conda changes md5sums for test
- path: results/preprocessing/markduplicates/test/test.md.bam.bai
- path: results/preprocessing/markduplicates/test2/test2.md.bam.bai
# conda changes md5sums for test
- path: results/preprocessing/recal_table/test/test.recal.table
- path: results/preprocessing/recal_table/test2/test2.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.bam
- path: results/preprocessing/recalibrated/test2/test2.recal.bam
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.bam.bai
- path: results/preprocessing/recalibrated/test2/test2.recal.bam.bai
# binary changes md5sums on reruns
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
- 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/test/test.md.mosdepth.global.dist.txt
md5sum: 9269e959d5eec5273307693c6274f53e
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
md5sum: deb2df4f3ca19f441f0a22f04dea8723
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
md5sum: 96acf3439477a1448b7e1b43c020c7d0
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
md5sum: c259a9fd73f576626c3a29841c2dc019
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
md5sum: cf85ba4692f016af70db2a594d9effdf
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
md5sum: 9269e959d5eec5273307693c6274f53e
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
md5sum: deb2df4f3ca19f441f0a22f04dea8723
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
md5sum: 96acf3439477a1448b7e1b43c020c7d0
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
md5sum: c259a9fd73f576626c3a29841c2dc019
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
md5sum: cf85ba4692f016af70db2a594d9effdf
- path: results/reports/samtools/test/test.md.cram.stats
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
md5sum: 85d38a74ce189b9110c57cd94bc26757
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
md5sum: 04b69ef7f00199dcea7822a79d2c7bd7
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
md5sum: 4e6c360aea7f05d801b2ea5685fe154a
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
md5sum: 5bf5fc178e4faf2462427502c3666004
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test