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Make lane Column Optional in Samplesheet#1943
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animesh wants to merge 1 commit intonf-core:devfrom
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Addressing the issue raised in #1942
Key changes:
- Schema: Removed all requirements and dependencies for
lane. - Docs: Updated to clarify
laneis optional; examples revised. - Example: Added minimal samplesheet without
lane; kept optional example. - Workflow: Logic updated to handle presence or absence of
lane.
Testing:
Pipeline tested without lane and it work as expected
...ple, and workflow logic
Member
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
FriederikeHanssen
requested changes
Jul 23, 2025
Contributor
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Can you please add a few nf-test tests? This column is quite important further in the workflow to ensure the right samples are grouped together before duplicate marking and ensureing we are not creating blocking conditions on the grouping
Author
thanks @FriederikeHanssen for checking, i have not done this before but i can give it a go, is there some tutorial to follow? |
Contributor
|
maybe check how we implement tests for other fucntionality in the pipeline in the tests/ folder. for a general introcution to nf-test, you can follow the training here: https://training.nextflow.io/latest/side_quests/nf-test/ It's obviously a lot simpler than how we use the testing but a good introduction to the general concepts. |
Author
|
Thanks for the pointers @FriederikeHanssen , i tried to intall nf-test via 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED (multi_intervals)'
Caused by:
Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED (multi_intervals)` terminated with an error exit status (127)
Command executed:
bgzip --threads 1 -c multi_intervals.bed > multi_intervals.bed.gz
tabix --threads 1 multi_intervals.bed.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED":
tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 2: bgzip: command not found
Work dir:
/home/ash022/nf-core-sarek/.nf-test/tests/66be0e22361ebaed1d 4168bfacf262b3/work/87/9dfd86c880b0ca5b44b3f585cd156e
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/66be0e22361ebaed1 d4168bfacf262b3/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/66be0e22361ebaed1 d4168bfacf262b3/meta/nextflow.log' file for details
Nextflow stderr:
Test [82570c02] 'Run with profile test | --tools controlfreec --no_intervals | tumoronly' Assertion failed:
assert workflow.success
| |
workflow false
java.lang.RuntimeException: Different Snapshot:
[ [
11, | 0,
{ {
"ASSESS_SIGNIFICANCE": { <
"controlfreec": 11.6 <
}, <
"FREEC2BED": { <
"controlfreec": "11.6b" <
}, <
"FREEC2CIRCOS": { <
"controlfreec": "11.6b" <
}, <
"FREEC_TUMORONLY": { <
"controlfreec": "11.6b" <
}, <
"MAKEGRAPH2": { <
"controlfreec": "11.6b" <
}, <
"SAMTOOLS_MPILEUP": { <
"samtools": 1.21 <
}, <
"Workflow": { "Workflow": {
"nf-core/sarek": "v3.5.1" "nf-core/sarek": "v3.5.1"
} }
}, },
[ [
"csv", "csv",
"multiqc", <
"multiqc/multiqc_data", <
"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_report.html", <
"no_intervals.bed", "no_intervals.bed",
"no_intervals.bed.gz", "no_intervals.bed.gz",
"no_intervals.bed.gz.tbi", "no_intervals.bed.gz.tbi",
"pipeline_info", "pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml", | "pipeline_info/nf_core_sarek_software_mqc_versions.yml"
"reference", <
"reports", <
"reports/mosdepth", <
"reports/mosdepth/sample2", <
"reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist .txt", <
"reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt ", <
"reports/mosdepth/sample2/sample2.recal.per-base.bed.gz", <
"reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi" , <
"reports/samtools", <
"reports/samtools/sample2", <
"reports/samtools/sample2/sample2.recal.cram.stats", <
"variant_calling", <
"variant_calling/controlfreec", <
"variant_calling/controlfreec/sample2", <
"variant_calling/controlfreec/sample2/config.txt", <
"variant_calling/controlfreec/sample2/sample2.bed", <
"variant_calling/controlfreec/sample2/sample2.circos.txt", <
"variant_calling/controlfreec/sample2/sample2.p.value.txt", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_BAF.txt", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_CNVs", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_info.txt", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_ratio.BedGraph", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_ratio.txt", <
"variant_calling/controlfreec/sample2/sample2.tumor.mpileup. gz_sample.cpn", <
"variant_calling/controlfreec/sample2/sample2_BAF.png", <
"variant_calling/controlfreec/sample2/sample2_ratio.log2.png ", <
"variant_calling/controlfreec/sample2/sample2_ratio.png" <
], ],
[ [
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" , |
"sample2.recal.mosdepth.global.dist.txt:md5,f2dcd00a64947c49 e8e4b93c2f4fbf27", <
"sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c75 64f00aa000f0", <
"sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe9 4cb676c", <
"sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca 249b8b58eb9", <
"sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd 03", <
"sample2.bed:md5,5249f46e614b60867bdd6b9b83327979", <
"sample2.circos.txt:md5,2efab24d023931cec8b158c56d1f1765", <
"sample2.p.value.txt:md5,38c8c9ad33a4fca3804a34d5c436cd1e", <
"sample2.tumor.mpileup.gz_BAF.txt:md5,0bb91da6a637ed64d7622e b7d539fd71", <
"sample2.tumor.mpileup.gz_CNVs:md5,741831784091e9a51e0c07117 b67e18f", <
"sample2.tumor.mpileup.gz_info.txt:md5,fed6aa0e0f4232255d515 2f5774161b9", <
"sample2.tumor.mpileup.gz_ratio.BedGraph:md5,d2347daecbb4eb1 f1a3b5558acdf657a", <
"sample2.tumor.mpileup.gz_ratio.txt:md5,7587b17b4303715aa45e ae017e357c23", <
"sample2.tumor.mpileup.gz_sample.cpn:md5,8bf25e5cf94e89bcbbd 4bb0d453d3057", <
"sample2_BAF.png:md5,32e1189f07f9ddb4892cae10f4003e4a", <
"sample2_ratio.log2.png:md5,6d8b8cabc35d391f9a92ede6128eb378 ", <
"sample2_ratio.png:md5,47fce58116c63d6cad34f80575e34e43" <
], ],
[ [
] ]
] ]
FAILED (39.192s)
Assertion failed:
2 of 2 assertions failed
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED (no_intervals)'
Caused by:
Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED (no_intervals)` terminated with an error exit status (127)
Command executed:
bgzip --threads 1 -c no_intervals.bed > no_intervals.bed.gz
tabix --threads 1 no_intervals.bed.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_CO MBINED":
tabix: $(echo $(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 2: bgzip: command not found
Work dir:
/home/ash022/nf-core-sarek/.nf-test/tests/82570c021470b7ee52 402a284974891b/work/ea/41a54c4b07ad8d1397a69499cf1e31
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/82570c021470b7ee5 2402a284974891b/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/82570c021470b7ee5 2402a284974891b/meta/nextflow.log' file for details
Nextflow stderr:
Test [c2460de9] 'Run with profile test | --tools controlfreec --no_intervals | somatic | stub' Assertion failed:
assert workflow.success
| |
workflow false
java.lang.RuntimeException: Different Snapshot:
[ [
14, | 8,
{ {
"ASSESS_SIGNIFICANCE": { <
"controlfreec": 11.6 <
}, <
"FREEC2BED": { <
"controlfreec": "11.6b" <
}, <
"FREEC2CIRCOS": { <
"controlfreec": "11.6b" <
}, <
"FREEC_SOMATIC": { <
"controlfreec": "11.6b" <
}, <
"MAKEGRAPH2": { <
"controlfreec": "11.6b" <
}, <
"SAMTOOLS_MPILEUP": { <
"samtools": 1.21 <
}, <
"Workflow": { "Workflow": {
"nf-core/sarek": "v3.5.1" "nf-core/sarek": "v3.5.1"
} }
}, },
[ [
"csv", "csv",
"multiqc", <
"multiqc/multiqc_data", <
"multiqc/multiqc_plots", <
"multiqc/multiqc_report.html", <
"no_intervals.bed", "no_intervals.bed",
"no_intervals.bed.gz", "no_intervals.bed.gz",
"no_intervals.bed.gz.tbi", "no_intervals.bed.gz.tbi",
"pipeline_info", "pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml", "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reference", "reference",
"reports", "reports",
"reports/mosdepth", "reports/mosdepth",
"reports/mosdepth/sample3", "reports/mosdepth/sample3",
"reports/mosdepth/sample3/sample3.recal.global.dist.txt", "reports/mosdepth/sample3/sample3.recal.global.dist.txt",
"reports/mosdepth/sample3/sample3.recal.per-base.bed.gz", "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz",
"reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi" , "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi" ,
"reports/mosdepth/sample3/sample3.recal.per-base.d4", "reports/mosdepth/sample3/sample3.recal.per-base.d4",
"reports/mosdepth/sample3/sample3.recal.quantized.bed.gz", "reports/mosdepth/sample3/sample3.recal.quantized.bed.gz",
"reports/mosdepth/sample3/sample3.recal.quantized.bed.gz.csi ", "reports/mosdepth/sample3/sample3.recal.quantized.bed.gz.csi ",
"reports/mosdepth/sample3/sample3.recal.region.dist.txt", "reports/mosdepth/sample3/sample3.recal.region.dist.txt",
"reports/mosdepth/sample3/sample3.recal.regions.bed.gz", "reports/mosdepth/sample3/sample3.recal.regions.bed.gz",
"reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi", "reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi",
"reports/mosdepth/sample3/sample3.recal.summary.txt", "reports/mosdepth/sample3/sample3.recal.summary.txt",
"reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz", "reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz",
"reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz.cs i", "reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz.cs i",
"reports/mosdepth/sample4", "reports/mosdepth/sample4",
"reports/mosdepth/sample4/sample4.recal.global.dist.txt", "reports/mosdepth/sample4/sample4.recal.global.dist.txt",
"reports/mosdepth/sample4/sample4.recal.per-base.bed.gz", "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz",
"reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi" , "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi" ,
"reports/mosdepth/sample4/sample4.recal.per-base.d4", "reports/mosdepth/sample4/sample4.recal.per-base.d4",
"reports/mosdepth/sample4/sample4.recal.quantized.bed.gz", "reports/mosdepth/sample4/sample4.recal.quantized.bed.gz",
"reports/mosdepth/sample4/sample4.recal.quantized.bed.gz.csi ", "reports/mosdepth/sample4/sample4.recal.quantized.bed.gz.csi ",
"reports/mosdepth/sample4/sample4.recal.region.dist.txt", "reports/mosdepth/sample4/sample4.recal.region.dist.txt",
"reports/mosdepth/sample4/sample4.recal.regions.bed.gz", "reports/mosdepth/sample4/sample4.recal.regions.bed.gz",
"reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi", "reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi",
"reports/mosdepth/sample4/sample4.recal.summary.txt", "reports/mosdepth/sample4/sample4.recal.summary.txt",
"reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz", "reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz",
"reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz.cs i", "reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz.cs i",
"reports/samtools", "reports/samtools",
"reports/samtools/sample3", "reports/samtools/sample3",
"reports/samtools/sample3/sample3.recal.cram.stats", "reports/samtools/sample3/sample3.recal.cram.stats",
"reports/samtools/sample4", "reports/samtools/sample4",
"reports/samtools/sample4/sample4.recal.cram.stats", | "reports/samtools/sample4/sample4.recal.cram.stats"
"variant_calling", <
"variant_calling/controlfreec", <
"variant_calling/controlfreec/sample4_vs_sample3", <
"variant_calling/controlfreec/sample4_vs_sample3/GC_profile. sample4_vs_sample3.cpn", <
"variant_calling/controlfreec/sample4_vs_sample3/config.txt" , <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3.bed", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3.circos.txt", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3.p.value.txt", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_BAF.png", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_BAF.txt", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_CNVs", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_info.txt", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_ratio.BedGraph", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_ratio.log2.png", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_ratio.png", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_ratio.txt", <
"variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_ sample3_sample.cpn" <
], ],
[ [
"sample3.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample3.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample3.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940", "sample3.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940",
"sample3.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e", "sample3.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e",
"sample3.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample3.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample3.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940", "sample3.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940",
"sample3.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e", "sample3.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e",
"sample3.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample3.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample3.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940", "sample3.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940",
"sample3.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e", "sample3.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e",
"sample3.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample3.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample3.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940", "sample3.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940",
"sample3.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e", "sample3.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e",
"sample4.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample4.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample4.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940", "sample4.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940",
"sample4.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e", "sample4.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e",
"sample4.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample4.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample4.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940", "sample4.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940",
"sample4.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e", "sample4.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e",
"sample4.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample4.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample4.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940", "sample4.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940",
"sample4.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e", "sample4.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e",
"sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940", "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940",
"sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e", "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e",
"sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e", "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e",
"sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e", | "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e"
"GC_profile.sample4_vs_sample3.cpn:md5,d41d8cd98f00b204e9800 998ecf8427e", <
"sample4_vs_sample3.bed:md5,d41d8cd98f00b204e9800998ecf8427e ", <
"sample4_vs_sample3.circos.txt:md5,d41d8cd98f00b204e9800998e cf8427e", <
"sample4_vs_sample3.p.value.txt:md5,d41d8cd98f00b204e9800998 ecf8427e", <
"sample4_vs_sample3_BAF.png:md5,d41d8cd98f00b204e9800998ecf8 427e", <
"sample4_vs_sample3_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8 427e", <
"sample4_vs_sample3_CNVs:md5,d41d8cd98f00b204e9800998ecf8427 e", <
"sample4_vs_sample3_info.txt:md5,d41d8cd98f00b204e9800998ecf 8427e", <
"sample4_vs_sample3_ratio.BedGraph:md5,d41d8cd98f00b204e9800 998ecf8427e", <
"sample4_vs_sample3_ratio.log2.png:md5,d41d8cd98f00b204e9800 998ecf8427e", <
"sample4_vs_sample3_ratio.png:md5,d41d8cd98f00b204e9800998ec f8427e", <
"sample4_vs_sample3_ratio.txt:md5,d41d8cd98f00b204e9800998ec f8427e", <
"sample4_vs_sample3_sample.cpn:md5,d41d8cd98f00b204e9800998e cf8427e" <
], ],
[ [
] ]
] ]
FAILED (47.706s)
Assertion failed:
2 of 2 assertions failed
Nextflow stdout:
ERROR ~ mapping values are not allowed here
in 'reader', line 2, column 140:
... e64be371b4f664505d51/.command.sh: line 4: samtools: command not ...
^
-- Check script '/home/ash022/nf-core-sarek/subworkflows/nf-core/utils_nfcor e_pipeline/main.nf' at line: 97 or see '/home/ash022/nf-core-sarek/.nf-test/tests/c2460de90a167c3bc 0db10145705422a/meta/nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/c2460de90a167c3bc 0db10145705422a/meta/nextflow.log' file for details
Nextflow stderr:
Test [e75ac9b0] 'Run with profile test | --tools controlfreec | tumoronly | stub' Assertion failed:
assert workflow.success
| |
workflow false
java.lang.RuntimeException: Different Snapshot:
[ [
13, | 7,
{ {
"ASSESS_SIGNIFICANCE": { <
"controlfreec": 11.6 <
}, <
"FREEC2BED": { <
"controlfreec": "11.6b" <
}, <
"FREEC2CIRCOS": { <
"controlfreec": "11.6b" <
}, <
"FREEC_TUMORONLY": { <
"controlfreec": "11.6b" <
}, <
"MAKEGRAPH2": { <
"controlfreec": "11.6b" <
}, <
"SAMTOOLS_MPILEUP": { <
"samtools": 1.21 <
}, <
"Workflow": { "Workflow": {
"nf-core/sarek": "v3.5.1" "nf-core/sarek": "v3.5.1"
} }
}, },
[ [
"csv", "csv",
"multiqc", <
"multiqc/multiqc_data", <
"multiqc/multiqc_plots", <
"multiqc/multiqc_report.html", <
"pipeline_info", "pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml", "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reference", "reference",
"reports", "reports",
"reports/mosdepth", "reports/mosdepth",
"reports/mosdepth/sample2", "reports/mosdepth/sample2",
"reports/mosdepth/sample2/sample2.recal.global.dist.txt", "reports/mosdepth/sample2/sample2.recal.global.dist.txt",
"reports/mosdepth/sample2/sample2.recal.per-base.bed.gz", "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz",
"reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi" , "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi" ,
"reports/mosdepth/sample2/sample2.recal.per-base.d4", "reports/mosdepth/sample2/sample2.recal.per-base.d4",
"reports/mosdepth/sample2/sample2.recal.quantized.bed.gz", "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz",
"reports/mosdepth/sample2/sample2.recal.quantized.bed.gz.csi ", "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz.csi ",
"reports/mosdepth/sample2/sample2.recal.region.dist.txt", "reports/mosdepth/sample2/sample2.recal.region.dist.txt",
"reports/mosdepth/sample2/sample2.recal.regions.bed.gz", "reports/mosdepth/sample2/sample2.recal.regions.bed.gz",
"reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi", "reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi",
"reports/mosdepth/sample2/sample2.recal.summary.txt", "reports/mosdepth/sample2/sample2.recal.summary.txt",
"reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz", "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz",
"reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz.cs i", "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz.cs i",
"reports/samtools", "reports/samtools",
"reports/samtools/sample2", "reports/samtools/sample2",
"reports/samtools/sample2/sample2.recal.cram.stats", | "reports/samtools/sample2/sample2.recal.cram.stats"
"variant_calling", <
"variant_calling/controlfreec", <
"variant_calling/controlfreec/sample2", <
"variant_calling/controlfreec/sample2/GC_profile.sample2.cpn ", <
"variant_calling/controlfreec/sample2/config.txt", <
"variant_calling/controlfreec/sample2/sample2.bed", <
"variant_calling/controlfreec/sample2/sample2.circos.txt", <
"variant_calling/controlfreec/sample2/sample2.p.value.txt", <
"variant_calling/controlfreec/sample2/sample2_BAF.png", <
"variant_calling/controlfreec/sample2/sample2_BAF.txt", <
"variant_calling/controlfreec/sample2/sample2_CNVs", <
"variant_calling/controlfreec/sample2/sample2_info.txt", <
"variant_calling/controlfreec/sample2/sample2_ratio.BedGraph ", <
"variant_calling/controlfreec/sample2/sample2_ratio.log2.png ", <
"variant_calling/controlfreec/sample2/sample2_ratio.png", <
"variant_calling/controlfreec/sample2/sample2_ratio.txt", <
"variant_calling/controlfreec/sample2/sample2_sample.cpn" <
], ],
[ [
"sample2.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample2.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940", "sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5 cb9c940",
"sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e", "sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800 998ecf8427e",
"sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940", "sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad 5cb9c940",
"sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e", "sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e980 0998ecf8427e",
"sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e", "sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998e cf8427e",
"sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940", "sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5c b9c940",
"sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e", "sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e98009 98ecf8427e",
"sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e", "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf84 27e",
"sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940", "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8a d5cb9c940",
"sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e", "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e98 00998ecf8427e",
"sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e", | "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf842 7e"
"GC_profile.sample2.cpn:md5,d41d8cd98f00b204e9800998ecf8427e ", <
"sample2.bed:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2.p.value.txt:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_BAF.png:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_CNVs:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_ratio.BedGraph:md5,d41d8cd98f00b204e9800998ecf8427e ", <
"sample2_ratio.log2.png:md5,d41d8cd98f00b204e9800998ecf8427e ", <
"sample2_ratio.png:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_ratio.txt:md5,d41d8cd98f00b204e9800998ecf8427e", <
"sample2_sample.cpn:md5,d41d8cd98f00b204e9800998ecf8427e" <
], ],
[ [
] ]
] ]
FAILED (42.557s)
Assertion failed:
2 of 2 assertions failed
Nextflow stdout:
ERROR ~ mapping values are not allowed here
in 'reader', line 2, column 140:
... d0566bda67cbe5909f38/.command.sh: line 4: samtools: command not ...
^
-- Check script '/home/ash022/nf-core-sarek/subworkflows/nf-core/utils_nfcor e_pipeline/main.nf' at line: 97 or see '/home/ash022/nf-core-sarek/.nf-test/tests/e75ac9b013a41c670 97c266c0d9a3140/meta/nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/ash022/nf-core-sarek/.nf-test/tests/e75ac9b013a41c670 97c266c0d9a3140/meta/nextflow.log' file for details
Nextflow stderr:
Snapshots:
Obsolete snapshots can only be checked if all tests of a file are executed successful.
FAILURE: Executed 4 tests in 175.187s (4 failed)
">
nf-test test tests/variant_calling_controlfreec.nf.test |
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