Implemented MSISENSORPRO tumor-only analysis #1737
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 2.14.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
| MSISENSORPRO_SCAN(fasta) | ||
| msisensorpro_scan = MSISENSORPRO_SCAN.out.list.map{ meta, list -> [list] } | ||
| versions = versions.mix(MSISENSORPRO_SCAN.out.versions) |
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Is this something we can put in the PREPARE* subworkflows together with other reference computations for tools?
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I did that first, but it was being generated unnecessarily if msi analysis was not requested. I couldn't find a way to avoid that in the PREPARE* subworkflows so left it like this.
| @@ -177,7 +189,7 @@ workflow NFCORE_SAREK { | |||
| rt_file = PREPARE_GENOME.out.rt_file | |||
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| // Tabix indexed vcf files | |||
| bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([]) | |||
| bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([]) | |||
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merged your PR, so If you merge in dev this should hopefully be fixed already
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Yes thanks for that, this is just shipped along.
| @@ -175,11 +174,10 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { | |||
| } | |||
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| // MSISENSOR | |||
| if (tools.split(',').contains('msisensorpro')) { | |||
| if (tools.split(',').contains('msisensorpro') && msisensorpro_scan) { | |||
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This should not be strictly necessary since the empty channel should skip the tool
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I remember I tried without it but it failed for some reason that I can't remember now so I think it was necessary.
| MSISENSORPRO_MSISOMATIC(cram.combine(intervals_bed_combined), fasta.map{ meta, fasta -> [ fasta ] }, msisensorpro_scan) | ||
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| versions = versions.mix(MSISENSORPRO_MSISOMATIC.out.versions) | ||
| out_msisensorpro = out_msisensorpro.mix(MSISENSORPRO_MSISOMATIC.out.output_report) |
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any reason you are not emitting the output of the workflow anymore?
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It's not used anywhere else, just published in the output directory. MultiQC does not support msisensorpro yet.
| @@ -109,6 +111,13 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL { | |||
| versions = versions.mix(BAM_VARIANT_CALLING_FREEBAYES.out.versions) | |||
| } | |||
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| // MSISENSOR | |||
| if (tools.split(',').contains('msisensorpro') && msisensorpro_baseline) { | |||
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similar here, if the baseline is require than the tool shouldn't run on an empty channel
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I remember I tried without it but it failed for some reason that I can't remember now so I think it was necessary.
| @@ -12,7 +12,6 @@ include { BWA_INDEX as BWAMEM1_INDEX } from '../../../modules/nf- | |||
| include { BWAMEM2_INDEX } from '../../../modules/nf-core/bwamem2/index/main' | |||
| include { DRAGMAP_HASHTABLE } from '../../../modules/nf-core/dragmap/hashtable/main' | |||
| include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' | |||
| include { MSISENSORPRO_SCAN } from '../../../modules/nf-core/msisensorpro/scan/main' | |||
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what is the reason to move this out?
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I moved it to main workflow file main.nf as it was unnecessarily generated if msisensorpro was not requested. As now I made msisensorpro_scan and msisensorpro_baseline optional params.
Implements #1599 and #330
MSIsensorpro now also works with tumor-only samples if a baseline is provided by the user:
msisensor-pro protumor-only analysis using the new module: Added new module: msisensorpro/msitumoronly modules#6350params.msisensorpro_baselinewill trigger tumor-only analysis independently from paired analysismsisensorpro_baseline: https://github.com/xjtu-omics/msisensor-pro/wiki/Best-Practicesmsisensorpro_scantoparamssupporting user-provided reference msi list for paired analysisPR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).