Skip to content

Commit

Permalink
rescue preparerecalibration tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@maxulysse
maxulysse committed Jan 29, 2025
1 parent 81e3925 commit e0261b7
Show file tree
Hide file tree
Showing 2 changed files with 144 additions and 116 deletions.
8 changes: 4 additions & 4 deletions tests/start_from_preparerecalibration.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ nextflow_pipeline {
tag "pipeline"
tag "pipeline_sarek"

test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null ") {
test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null") {

when {
params {
Expand Down Expand Up @@ -43,7 +43,7 @@ nextflow_pipeline {
}
}

test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") {
test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka") {

when {
params {
Expand Down Expand Up @@ -83,7 +83,7 @@ nextflow_pipeline {
}


test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ") {
test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null") {

when {
params {
Expand Down Expand Up @@ -121,7 +121,7 @@ nextflow_pipeline {
}
}

test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") {
test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka") {

when {
params {
Expand Down
252 changes: 140 additions & 112 deletions tests/start_from_preparerecalibration.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,72 +1,7 @@
{
"Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null ": {
"Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": {
"content": [
7,
{
"GATK4_APPLYBQSR": {
"gatk4": "4.5.0.0"
},
"GATK4_BASERECALIBRATOR": {
"gatk4": "4.5.0.0"
},
"Workflow": {
"nf-core/sarek": "v3.6.0dev"
}
},
[
"csv",
"csv/markduplicates.csv",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt",
"multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt",
"multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt",
"multiqc/multiqc_data/gatk_base_recalibrator.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-reported-empirical-plot.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-reported-empirical-plot.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"preprocessing",
"preprocessing/recal_table",
"preprocessing/recal_table/test",
"preprocessing/recal_table/test/test.recal.table",
"reference"
],
[
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
"multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9"
],
[

]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-09T16:57:10.392231"
},
"Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ": {
"content": [
10,
9,
{
"BCFTOOLS_STATS": {
"bcftools": 1.2
Expand Down Expand Up @@ -139,6 +74,10 @@
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reference",
"reference/intervals",
"reference/intervals/GRCh38_chr22.bed.gz",
"reference/intervals/chr22_1-40001.bed",
"reference/intervals/chr22_1-40001.bed.gz",
"reports",
"reports/bcftools",
"reports/bcftools/strelka",
Expand Down Expand Up @@ -168,23 +107,126 @@
"multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889",
"GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619",
"test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027",
"test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
],
[


]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-01-29T12:16:09.850612622"
},
"Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null": {
"content": [
9,
{
"GATK4_APPLYBQSR": {
"gatk4": "4.5.0.0"
},
"GATK4_BASERECALIBRATOR": {
"gatk4": "4.5.0.0"
},
"INDEX_CRAM": {
"samtools": 1.21
},
"Workflow": {
"nf-core/sarek": "v3.6.0dev"
}
},
[
"csv",
"csv/markduplicates.csv",
"csv/recalibrated.csv",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt",
"multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt",
"multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt",
"multiqc/multiqc_data/gatk_base_recalibrator.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf",
"multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png",
"multiqc/multiqc_plots/png/gatk-base-recalibrator-reported-empirical-plot.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.svg",
"multiqc/multiqc_plots/svg/gatk-base-recalibrator-reported-empirical-plot.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"preprocessing",
"preprocessing/recal_table",
"preprocessing/recal_table/test",
"preprocessing/recal_table/test/test.recal.table",
"preprocessing/recalibrated",
"preprocessing/recalibrated/test",
"preprocessing/recalibrated/test/test.recal.cram",
"preprocessing/recalibrated/test/test.recal.cram.crai",
"reference",
"reference/intervals",
"reference/intervals/GRCh38_chr22.bed.gz",
"reference/intervals/chr22_1-40001.bed",
"reference/intervals/chr22_1-40001.bed.gz",
"reports",
"reports/mosdepth",
"reports/mosdepth/test",
"reports/mosdepth/test/test.recal.mosdepth.global.dist.txt",
"reports/mosdepth/test/test.recal.mosdepth.region.dist.txt",
"reports/mosdepth/test/test.recal.mosdepth.summary.txt",
"reports/mosdepth/test/test.recal.regions.bed.gz",
"reports/mosdepth/test/test.recal.regions.bed.gz.csi",
"reports/samtools",
"reports/samtools/test",
"reports/samtools/test/test.recal.cram.stats"
],
[
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
"multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9",
"GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972",
"test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
"test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
"test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
"test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
"test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e"
],
[
[
"test.recal.cram",
"463ac3b905fbf4ddf113a94dbfa8d69f"
]
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-11-09T16:58:48.877928"
"timestamp": "2025-01-29T12:17:03.643548661"
},
"Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ": {
"Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": {
"content": [
10,
9,
{
"BCFTOOLS_STATS": {
"bcftools": 1.2
Expand Down Expand Up @@ -257,6 +299,10 @@
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reference",
"reference/intervals",
"reference/intervals/GRCh38_chr22.bed.gz",
"reference/intervals/chr22_1-40001.bed",
"reference/intervals/chr22_1-40001.bed.gz",
"reports",
"reports/bcftools",
"reports/bcftools/strelka",
Expand Down Expand Up @@ -286,41 +332,40 @@
"multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889",
"GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619",
"test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027",
"test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
],
[

]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-11-09T17:02:51.883814"
"timestamp": "2025-01-29T12:17:51.224786491"
},
"Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ": {
"Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null": {
"content": [
10,
6,
{
"GATK4_APPLYBQSR": {
"gatk4": "4.5.0.0"
},
"GATK4_BASERECALIBRATOR": {
"gatk4": "4.5.0.0"
},
"INDEX_CRAM": {
"samtools": 1.21
},
"Workflow": {
"nf-core/sarek": "v3.6.0dev"
}
},
[
"csv",
"csv/markduplicates.csv",
"csv/recalibrated.csv",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt",
Expand Down Expand Up @@ -352,45 +397,28 @@
"preprocessing/recal_table",
"preprocessing/recal_table/test",
"preprocessing/recal_table/test/test.recal.table",
"preprocessing/recalibrated",
"preprocessing/recalibrated/test",
"preprocessing/recalibrated/test/test.recal.cram",
"preprocessing/recalibrated/test/test.recal.cram.crai",
"reference",
"reports",
"reports/mosdepth",
"reports/mosdepth/test",
"reports/mosdepth/test/test.recal.mosdepth.global.dist.txt",
"reports/mosdepth/test/test.recal.mosdepth.region.dist.txt",
"reports/mosdepth/test/test.recal.mosdepth.summary.txt",
"reports/mosdepth/test/test.recal.regions.bed.gz",
"reports/mosdepth/test/test.recal.regions.bed.gz.csi",
"reports/samtools",
"reports/samtools/test",
"reports/samtools/test/test.recal.cram.stats"
"reference/intervals",
"reference/intervals/GRCh38_chr22.bed.gz",
"reference/intervals/chr22_1-40001.bed",
"reference/intervals/chr22_1-40001.bed.gz"
],
[
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
"gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
"multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9",
"test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972",
"test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
"test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
"test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
"test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
"test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e"
"GRCh38_chr22.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7",
"chr22_1-40001.bed.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
],
[
[
"test.recal.cram",
"463ac3b905fbf4ddf113a94dbfa8d69f"
]

]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-11-09T17:01:30.130705"
"timestamp": "2025-01-29T12:15:22.917095422"
}
}
}

0 comments on commit e0261b7

Please sign in to comment.