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Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #1728

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merged 10 commits into from
Nov 12, 2024
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Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #1728

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538f833
don't convert input bam files, it's not necessary. Tools are smart
FriederikeHanssen Nov 8, 2024
a4b517d
Add nf-test
FriederikeHanssen Nov 8, 2024
e8a7e81
remove local test file
FriederikeHanssen Nov 8, 2024
c1f45b7
skip pytests for new nf-test
FriederikeHanssen Nov 8, 2024
0a9561b
remove variable checksums
FriederikeHanssen Nov 9, 2024
bd2392f
remove variable checksums
FriederikeHanssen Nov 9, 2024
139bcc3
remove variable checksums
FriederikeHanssen Nov 9, 2024
a318777
Update tests/start_from_markduplicates.nf.test
FriederikeHanssen Nov 12, 2024
fe43d3a
Update tests/start_from_recalibration.nf.test
FriederikeHanssen Nov 12, 2024
e8639d0
Update tests/start_from_preparerecalibration.nf.test
FriederikeHanssen Nov 12, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
- [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
- [1728](https://github.com/nf-core/sarek/pull/1728) - Remove BAM to CRAM conversion of input files for post-alignment entry points

### Dependencies

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16 changes: 0 additions & 16 deletions conf/test/markduplicates_bam.config
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16 changes: 0 additions & 16 deletions conf/test/markduplicates_cram.config
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16 changes: 0 additions & 16 deletions conf/test/prepare_recalibration_bam.config
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16 changes: 0 additions & 16 deletions conf/test/prepare_recalibration_cram.config
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3 changes: 3 additions & 0 deletions tests/.nftignore
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Expand Up @@ -9,6 +9,7 @@ multiqc/multiqc_data/multiqc_picard_dups.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/picard_deduplication.txt
multiqc/multiqc_data/vcftools_tstv_by_qual.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
Expand All @@ -20,4 +21,6 @@ reports/fastqc/**/*_fastqc.{html,zip}
reports/markduplicates/**/*.md.cram.metrics
reports/snpeff/*/*_snpEff.csv
reports/snpeff/*/snpEff_summary.html
reports/vcftools/**/*.TsTv.qual
variant_calling/**/*.vcf.{gz,gz.tbi}
.DS_Store
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That should not be produce by Nextflow

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it ended up in my nf-test test files repeatedly

14 changes: 6 additions & 8 deletions tests/alignment_from_everything.nf.test.snap
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Expand Up @@ -306,7 +306,6 @@
"samtools-stats-dp.txt:md5,c94f4d3ffa3f510552f90e173fdd9f9d",
"samtools_alignment_plot.txt:md5,717f499a3543e7ee4c7a8454bf80aeca",
"vcftools_tstv_by_count.txt:md5,50efc5214fe2c39f21efb66a710d2ed6",
"vcftools_tstv_by_qual.txt:md5,911bc05c5169149dbb0b068f65b4274a",
"test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967",
"test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
"test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
Expand All @@ -321,17 +320,16 @@
"test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
"test.recal.cram.stats:md5,820d123e746d1abdc90fd8710828082e",
"test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
"test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883"
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-29T08:21:45.439696"
"timestamp": "2024-11-09T21:51:21.998984"
}
}
}
10 changes: 4 additions & 6 deletions tests/alignment_to_fastq.nf.test.snap
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Expand Up @@ -306,7 +306,6 @@
"samtools-stats-dp.txt:md5,c94f4d3ffa3f510552f90e173fdd9f9d",
"samtools_alignment_plot.txt:md5,717f499a3543e7ee4c7a8454bf80aeca",
"vcftools_tstv_by_count.txt:md5,50efc5214fe2c39f21efb66a710d2ed6",
"vcftools_tstv_by_qual.txt:md5,911bc05c5169149dbb0b068f65b4274a",
"test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967",
"test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
"test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
Expand All @@ -321,17 +320,16 @@
"test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
"test.recal.cram.stats:md5,820d123e746d1abdc90fd8710828082e",
"test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
"test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883"
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-29T08:27:17.515894"
"timestamp": "2024-11-09T17:49:40.35031"
}
}
43 changes: 0 additions & 43 deletions tests/config/pytesttags.yml
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Expand Up @@ -35,21 +35,6 @@ sentieon/bwamem:
- tests/csv/3.0/fastq_single.csv
- tests/test_sentieon_aligner_bwamem.yml

## markduplicates
gatk4/markduplicates:
- conf/modules/markduplicates.config
- modules/nf-core/gatk4/markduplicates/**
- modules/nf-core/mosdepth/**
- modules/nf-core/samtools/convert/**
- modules/nf-core/samtools/index/**
- modules/nf-core/samtools/stats/**
- subworkflows/local/bam_markduplicates/**
- subworkflows/local/cram_qc_mosdepth_samtools/**
- tests/csv/3.0/mapped_single_bam.csv
- tests/csv/3.0/mapped_single_cram.csv
- tests/test_markduplicates_from_bam.yml
- tests/test_markduplicates_from_cram.yml

## sentieon/dedup
sentieon/dedup:
- conf/modules/sentieon_dedup.config
Expand All @@ -64,34 +49,6 @@ sentieon/dedup:
- tests/test_sentieon_dedup_from_bam.yml
- tests/test_sentieon_dedup_from_cram.yml

## prepare_recalibration
prepare_recalibration:
- conf/modules/prepare_recalibration.config
- modules/nf-core/gatk4/baserecalibrator/**
- modules/nf-core/gatk4/gatherbqsrreports/**
- modules/nf-core/mosdepth/**
- modules/nf-core/samtools/convert/**
- subworkflows/local/bam_baserecalibrator/**
- tests/csv/3.0/mapped_single_bam.csv
- tests/csv/3.0/mapped_single_cram.csv
- tests/test_prepare_recalibration_from_bam.yml
- tests/test_prepare_recalibration_from_cram.yml

## recalibrate
recalibrate:
- conf/modules/recalibrate.config
- modules/nf-core/gatk4/applybqsr/**
- modules/nf-core/samtools/convert/**
- modules/nf-core/samtools/index/**
- modules/nf-core/samtools/merge/**
- modules/nf-core/mosdepth/**
- subworkflows/local/bam_applybqsr/**
- subworkflows/local/cram_merge_index_samtools/**
- tests/csv/3.0/prepare_recalibration_single_bam.csv
- tests/csv/3.0/prepare_recalibration_single_cram.csv
- tests/test_recalibrate_from_bam.yml
- tests/test_recalibrate_from_cram.yml

## intervals
intervals:
- conf/modules/prepare_intervals.config
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8 changes: 3 additions & 5 deletions tests/default.nf.test.snap
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Expand Up @@ -289,7 +289,6 @@
"samtools-stats-dp.txt:md5,c94f4d3ffa3f510552f90e173fdd9f9d",
"samtools_alignment_plot.txt:md5,717f499a3543e7ee4c7a8454bf80aeca",
"vcftools_tstv_by_count.txt:md5,50efc5214fe2c39f21efb66a710d2ed6",
"vcftools_tstv_by_qual.txt:md5,911bc05c5169149dbb0b068f65b4274a",
"test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967",
"test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
"test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
Expand All @@ -304,8 +303,7 @@
"test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
"test.recal.cram.stats:md5,820d123e746d1abdc90fd8710828082e",
"test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
"test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883"
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
],
[
[
Expand All @@ -320,8 +318,8 @@
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.09.0"
"nextflow": "24.04.4"
},
"timestamp": "2024-10-08T12:09:25.505363"
"timestamp": "2024-11-09T21:41:27.897118"
}
}
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