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multiqc
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@maxulysse
maxulysse committed Sep 20, 2023
1 parent 40128c7 commit 0bf28e0
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Showing 3 changed files with 70 additions and 70 deletions.
9 changes: 5 additions & 4 deletions subworkflows/local/bam_sort_samtools/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -37,16 +37,17 @@ workflow BAM_SORT_SAMTOOLS {
}
.set { ch_bam_bai }

BAM_STATS_SAMTOOLS (
ch_bam_bai
)
BAM_STATS_SAMTOOLS(ch_bam_bai)

reports = BAM_STATS_SAMTOOLS.out.reports.map{meta, logs -> [logs] }

ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first())

emit:
bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ]
bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ]
csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ]

reports = BAM_STATS_SAMTOOLS.out.reports
reports
versions = ch_versions // channel: [ versions.yml ]
}
7 changes: 6 additions & 1 deletion subworkflows/local/bam_stats_samtools/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ workflow BAM_STATS_SAMTOOLS {

main:
ch_versions = Channel.empty()
ch_reports = Channel.empty()

SAMTOOLS_FLAGSTAT(ch_bam_bai)
SAMTOOLS_IDXSTATS(ch_bam_bai)
Expand All @@ -21,7 +22,11 @@ workflow BAM_STATS_SAMTOOLS {
ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first())
ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())

ch_reports = ch_reports.mix(SAMTOOLS_STATS.out.stats)
ch_reports = ch_reports.mix(SAMTOOLS_FLAGSTAT.out.flagstat)
ch_reports = ch_reports.mix(SAMTOOLS_IDXSTATS.out.idxstats)

emit:
reports = SAMTOOLS_STATS.out.stats.mix(SAMTOOLS_FLAGSTAT.out.flagstat, SAMTOOLS_IDXSTATS.out.idxstats)
reports = ch_reports
versions = ch_versions // channel: [ versions.yml ]
}
124 changes: 59 additions & 65 deletions workflows/rnavar.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ workflow RNAVAR {

// MODULE: Generate QC summary using FastQC
FASTQC(ch_cat_fastq)
ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs })
ch_versions = ch_versions.mix(FASTQC.out.versions.first())

//
Expand Down Expand Up @@ -426,39 +426,39 @@ workflow RNAVAR {

}

// //
// // MODULE: Index the VCF using TABIX
// //
// TABIX(ch_haplotypecaller_vcf)
//
// MODULE: Index the VCF using TABIX
//
TABIX(ch_haplotypecaller_vcf)

ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf
.join(TABIX.out.tbi, remainder: true)
.join(TABIX.out.csi, remainder: true)
.map{meta, vcf, tbi, csi ->
if (tbi) [meta, vcf, tbi]
else [meta, vcf, csi]
}

// ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf
// .join(TABIX.out.tbi, remainder: true)
// .join(TABIX.out.csi, remainder: true)
// .map{meta, vcf, tbi, csi ->
// if (tbi) [meta, vcf, tbi]
// else [meta, vcf, csi]
// }
ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null))
ch_final_vcf = ch_haplotypecaller_vcf

// ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null))
// ch_final_vcf = ch_haplotypecaller_vcf
//
// MODULE: VariantFiltration from GATK4
// Filter variant calls based on certain criteria
//
if (!params.skip_variantfiltration && !params.bam_csi_index ) {

// //
// // MODULE: VariantFiltration from GATK4
// // Filter variant calls based on certain criteria
// //
// if (!params.skip_variantfiltration && !params.bam_csi_index ) {

// GATK4_VARIANTFILTRATION(
// ch_haplotypecaller_vcf_tbi,
// ch_fasta,
// ch_fasta_fai,
// ch_dict
// )

// ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf
// ch_final_vcf = ch_filtered_vcf
// ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null))
// }
GATK4_VARIANTFILTRATION(
ch_haplotypecaller_vcf_tbi,
ch_fasta,
ch_fasta_fai.map{ it -> [ [id:'fai'], it ] },
ch_dict
)

ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf
ch_final_vcf = ch_filtered_vcf
ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null))
}

// //
// // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled.
Expand All @@ -481,40 +481,34 @@ workflow RNAVAR {

}

// ch_version_yaml = Channel.empty()
// CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml'))
// ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()

// //
// // MODULE: MultiQC
// // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report
// //
// if (!params.skip_multiqc){
// workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params)
// ch_workflow_summary = Channel.value(workflow_summary)

// methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
// ch_methods_description = Channel.value(methods_description)

// ch_multiqc_files = Channel.empty()
// ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
// ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
// ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
// ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
// ch_multiqc_files = ch_multiqc_files.mix(ch_version_yaml)
// ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
// ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect())
// ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config)
// ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo)

// MULTIQC(
// ch_multiqc_files.collect(),
// ch_multiqc_config.toList(),
// ch_multiqc_custom_config.toList(),
// ch_multiqc_logo.toList()
// )
// multiqc_report = MULTIQC.out.report.toList()
// }
ch_version_yaml = Channel.empty()
CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml'))
ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()

//
// MODULE: MultiQC
// Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report
//
if (!params.skip_multiqc){
workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)

methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
ch_methods_description = Channel.value(methods_description)

ch_reports.view()

multiqc_files = Channel.empty()
multiqc_files = multiqc_files.mix(ch_version_yaml)
multiqc_files = multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
multiqc_files = multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
multiqc_files = multiqc_files.mix(ch_reports.collect().ifEmpty([]))

MULTIQC(multiqc_files.collect(), ch_multiqc_config.collect().ifEmpty([]), ch_multiqc_custom_config.collect().ifEmpty([]), ch_multiqc_logo.collect().ifEmpty([]))

multiqc_report = MULTIQC.out.report.toList()
ch_versions = ch_versions.mix(MULTIQC.out.versions)
}
}

/*
Expand Down

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