Make `lane` Column Optional in Samplesheet by animesh · Pull Request #1943 · nf-core/sarek

animesh · 2025-07-21T13:49:00Z

Addressing the issue raised in #1942

Key changes:

Schema: Removed all requirements and dependencies for lane.
Docs: Updated to clarify lane is 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

nf-core-bot · 2025-07-21T13:49:38Z

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.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

FriederikeHanssen

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

animesh · 2025-07-23T12:03:46Z

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

thanks @FriederikeHanssen for checking, i have not done this before but i can give it a go, is there some tutorial to follow?

FriederikeHanssen · 2025-07-29T14:38:59Z

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.

animesh · 2025-08-05T11:29:18Z

Thanks for the pointers @FriederikeHanssen , i tried to intall nf-test via curl -fsSL https://get.nf-test.com | bash and run over the nf-core/sarek via git clone https://github.com/nf-core/sarek over one f the test files (details below) but it failed? I guess i am doing something wrong in testing the tests? Is there some working example specific to sarek pipeline which i can test and then use it as starting point to create test for no-lane sample-sheets?

nf-test test tests/variant_calling_controlfreec.nf.test

🚀 nf-test 0.9.2
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-bam/0.4.0/nft-bam-0.4.0.jar
Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/fgbio/callmolecularconsensusreads/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/fgbio/callmolecularconsensusreads/tests/../../sortbam/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/ngscheckmate/ncm/tests/../../../bedtools/makewindows/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/../../bwaindex/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/../../bwaindex/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/../../bwaindex/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/../../bwaindex/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/bwamem/tests/../../bwaindex/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/sentieon/haplotyper/tests/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/sentieon/haplotyper/tests/../../qualcal/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/../../compress/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/../../compress/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/../../compress/main.nf' not found.
Warning: Module /home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/main.nf.test: Dependency '/home/ash022/nf-core-sarek/modules/nf-core/spring/decompress/test/../../compress/main.nf' not found.

Test pipeline

  Test [66be0e22] 'Run with profile test | --tools controlfreec | somatic' Assertion failed: 

assert workflow.success
       |        |
       workflow false

java.lang.RuntimeException: Different Snapshot:
[                                                                                                       [
    16,                                                                                            |        1,
    {                                                                                                       {
        "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_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",                                                             <
        "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/mosdepth",                                                                        <
        "reports/mosdepth/sample3",                                                                <
        "reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt",                         <
        "reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt",                         <
        "reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt",                             <
        "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz",                                  <
        "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi",                              <
        "reports/mosdepth/sample3/sample3.recal.regions.bed.gz",                                   <
        "reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi",                               <
        "reports/mosdepth/sample4",                                                                <
        "reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt",                         <
        "reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt",                         <
        "reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt",                             <
        "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz",                                  <
        "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi",                              <
        "reports/mosdepth/sample4/sample4.recal.regions.bed.gz",                                   <
        "reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi",                               <
        "reports/samtools",                                                                        <
        "reports/samtools/sample3",                                                                <
        "reports/samtools/sample3/sample3.recal.cram.stats",                                       <
        "reports/samtools/sample4",                                                                <
        "reports/samtools/sample4/sample4.recal.cram.stats",                                       <
        "variant_calling",                                                                         <
        "variant_calling/controlfreec",                                                            <
        "variant_calling/controlfreec/sample4_vs_sample3",                                         <
        "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.normal.mpileup.gz_co   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt",          <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNV   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_inf   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_rat   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_rat   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sam   <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png",              <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png",       <
        "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png"             <
    ],                                                                                                      ],
    [                                                                                                       [
        "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",                              |            
        "sample3.recal.mosdepth.global.dist.txt:md5,69e29702ef01fd8f6c7a5468fc35a16a",             <
        "sample3.recal.mosdepth.region.dist.txt:md5,6ec49cd7d510c2eb3d9d90fdb79b783a",             <
        "sample3.recal.mosdepth.summary.txt:md5,103098d0bf76ed82d2b87d5f242b099a",                 <
        "sample3.recal.per-base.bed.gz:md5,297f96648928d0ca5184223fb9941e7c",                      <
        "sample3.recal.per-base.bed.gz.csi:md5,519cc5bf84da0d71b87a88c76f83194e",                  <
        "sample3.recal.regions.bed.gz:md5,314ce8d7273eff353072108aa77c327c",                       <
        "sample3.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",                   <
        "sample4.recal.mosdepth.global.dist.txt:md5,f2dcd00a64947c49e8e4b93c2f4fbf27",             <
        "sample4.recal.mosdepth.region.dist.txt:md5,39005ffaac22871ffaaf19656fe69c5b",             <
        "sample4.recal.mosdepth.summary.txt:md5,68d4b98f17361fddf73052ead34fa370",                 <
        "sample4.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",                      <
        "sample4.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",                  <
        "sample4.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",                       <
        "sample4.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",                   <
        "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",                           <
        "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",                           <
        "sample4_vs_sample3.bed:md5,47f60179409e9389e59b2e2525e42210",                             <
        "sample4_vs_sample3.circos.txt:md5,68addb1d8bda08355842bef0ab15cd6e",                      <
        "sample4_vs_sample3.normal.mpileup.gz_control.cpn:md5,d50bf2c9a4d35f022364901c284e80ed",   <
        "sample4_vs_sample3.p.value.txt:md5,3fad51341e7ee56c3b02de6a51d77efa",                     <
        "sample4_vs_sample3.tumor.mpileup.gz_BAF.txt:md5,723779bd103b66dcfa6fcfa692135a61",        <
        "sample4_vs_sample3.tumor.mpileup.gz_CNVs:md5,1d9166f66bf72adf2aea74adfc4ab015",           <
        "sample4_vs_sample3.tumor.mpileup.gz_info.txt:md5,b79da6ae026d86777d60d9f9edb9c6f6",       <
        "sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph:md5,cb087117ea046a6350885a34cb4bf667   <
        "sample4_vs_sample3.tumor.mpileup.gz_ratio.txt:md5,690cbefd87a77a6a37689135585c401c",      <
        "sample4_vs_sample3.tumor.mpileup.gz_sample.cpn:md5,b4f97163fdb6a3d97ca4ea560394cdb1",     <
        "sample4_vs_sample3_BAF.png:md5,16456932bb16e79c8cec4f747846c321",                         <
        "sample4_vs_sample3_ratio.log2.png:md5,89dce170acbb4c438be8359d242940df",                  <
        "sample4_vs_sample3_ratio.png:md5,6ac35ba93babc019c2d863f7e06b49b1"                        <
    ],                                                                                                      ],
    [                                                                                                       [
                                                                                                                
    ]                                                                                                       ]
]                                                                                                       ]

FAILED (45.715s)

  Assertion failed: 
  
  2 of 2 assertions failed
  
  Nextflow stdout:
  
  ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (multi_intervals)'
  
  Caused by:
    Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (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_COMBINED":
        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/66be0e22361ebaed1d4168bfacf262b3/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/66be0e22361ebaed1d4168bfacf262b3/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/66be0e22361ebaed1d4168bfacf262b3/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,f2dcd00a64947c49e8e4b93c2f4fbf27",             <
        "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",                 <
        "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",                      <
        "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",                  <
        "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",                           <
        "sample2.bed:md5,5249f46e614b60867bdd6b9b83327979",                                        <
        "sample2.circos.txt:md5,2efab24d023931cec8b158c56d1f1765",                                 <
        "sample2.p.value.txt:md5,38c8c9ad33a4fca3804a34d5c436cd1e",                                <
        "sample2.tumor.mpileup.gz_BAF.txt:md5,0bb91da6a637ed64d7622eb7d539fd71",                   <
        "sample2.tumor.mpileup.gz_CNVs:md5,741831784091e9a51e0c07117b67e18f",                      <
        "sample2.tumor.mpileup.gz_info.txt:md5,fed6aa0e0f4232255d5152f5774161b9",                  <
        "sample2.tumor.mpileup.gz_ratio.BedGraph:md5,d2347daecbb4eb1f1a3b5558acdf657a",            <
        "sample2.tumor.mpileup.gz_ratio.txt:md5,7587b17b4303715aa45eae017e357c23",                 <
        "sample2.tumor.mpileup.gz_sample.cpn:md5,8bf25e5cf94e89bcbbd4bb0d453d3057",                <
        "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_COMBINED (no_intervals)'
  
  Caused by:
    Process `NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (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_COMBINED":
        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/82570c021470b7ee52402a284974891b/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/82570c021470b7ee52402a284974891b/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/82570c021470b7ee52402a284974891b/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.csi",                                         "reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz.csi",
        "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.csi",                                         "reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz.csi",
        "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,d41d8cd98f00b204e9800998ecf8427e",                                   "sample3.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                   "sample3.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample3.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                               "sample3.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample3.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                  "sample3.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample3.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                              "sample3.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                   "sample3.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                    "sample3.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample3.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                                "sample3.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample3.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                 "sample3.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample3.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                             "sample3.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                   "sample4.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                   "sample4.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample4.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                               "sample4.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample4.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                  "sample4.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample4.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                              "sample4.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                   "sample4.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                    "sample4.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample4.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                                "sample4.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                 "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                             "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",                                        "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",                           |            "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
        "GC_profile.sample4_vs_sample3.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",                  <
        "sample4_vs_sample3.bed:md5,d41d8cd98f00b204e9800998ecf8427e",                             <
        "sample4_vs_sample3.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                      <
        "sample4_vs_sample3.p.value.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                     <
        "sample4_vs_sample3_BAF.png:md5,d41d8cd98f00b204e9800998ecf8427e",                         <
        "sample4_vs_sample3_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                         <
        "sample4_vs_sample3_CNVs:md5,d41d8cd98f00b204e9800998ecf8427e",                            <
        "sample4_vs_sample3_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                        <
        "sample4_vs_sample3_ratio.BedGraph:md5,d41d8cd98f00b204e9800998ecf8427e",                  <
        "sample4_vs_sample3_ratio.log2.png:md5,d41d8cd98f00b204e9800998ecf8427e",                  <
        "sample4_vs_sample3_ratio.png:md5,d41d8cd98f00b204e9800998ecf8427e",                       <
        "sample4_vs_sample3_ratio.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                       <
        "sample4_vs_sample3_sample.cpn:md5,d41d8cd98f00b204e9800998ecf8427e"                       <
    ],                                                                                                      ],
    [                                                                                                       [
                                                                                                                
    ]                                                                                                       ]
]                                                                                                       ]

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_nfcore_pipeline/main.nf' at line: 97 or see '/home/ash022/nf-core-sarek/.nf-test/tests/c2460de90a167c3bc0db10145705422a/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/c2460de90a167c3bc0db10145705422a/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.csi",                                         "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz.csi",
        "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,d41d8cd98f00b204e9800998ecf8427e",                                   "sample2.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                   "sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                               "sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                  "sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                              "sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                   "sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                    "sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                                "sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",                                       "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",                                 "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
        "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",                             "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
        "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",                           |            "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
        "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_nfcore_pipeline/main.nf' at line: 97 or see '/home/ash022/nf-core-sarek/.nf-test/tests/e75ac9b013a41c67097c266c0d9a3140/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/e75ac9b013a41c67097c266c0d9a3140/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)

Make 'lane' column in samplesheet optional: update schema, docs, exam…

b173733

…ple, and workflow logic

animesh requested review from FriederikeHanssen and maxulysse as code owners July 21, 2025 13:49

animesh enabled auto-merge July 22, 2025 07:50

FriederikeHanssen requested changes Jul 23, 2025

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FriederikeHanssen disabled auto-merge July 23, 2025 09:57

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Make `lane` Column Optional in Samplesheet#1943

Make `lane` Column Optional in Samplesheet#1943
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