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MultiQC update: alignment stats and software versions. #7

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merged 2 commits into from
Jul 16, 2024
Merged

MultiQC update: alignment stats and software versions. #7

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36825d7
Collect and report training and alignment statistics.
charles-plessy Jul 16, 2024
a2e223a
Collect more software version numbers.
charles-plessy Jul 16, 2024
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16 changes: 16 additions & 0 deletions assets/multiqc_config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,3 +13,19 @@ report_section_order:
export_plots: true

disable_version_detection: true

custom_data:
train:
file_format: "tsv"
section_name: "Training parameter statistics"
plot_type: "table"
last_o2o:
file_format: "tsv"
section_name: "Alignment statistics"
plot_type: "table"

sp:
last_o2o:
fn: "*o2o_aln.tsv"
train:
fn: "*train.tsv"
4 changes: 4 additions & 0 deletions subworkflows/local/pairalign_m2m/main.nf
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Expand Up @@ -115,10 +115,14 @@ workflow PAIRALIGN_M2M {

emit:

multiqc = Channel.empty()
.mix( LAST_TRAIN.out.multiqc.collect{ it[1]} )
.mix(LAST_SPLIT_O2O.out.multiqc.collect{ it[1]} )
m2m = LAST_LASTAL_M2M.out.maf
m2o = LAST_SPLIT_M2O.out.maf
o2m = LAST_SPLIT_O2M.out.maf
o2o = LAST_SPLIT_O2O.out.maf
versions = LAST_LASTDB.out.versions
}

/*
Expand Down
4 changes: 4 additions & 0 deletions subworkflows/local/pairalign_m2o/main.nf
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Expand Up @@ -77,8 +77,12 @@ workflow PAIRALIGN_M2O {

emit:

multiqc = Channel.empty()
.mix( LAST_TRAIN.out.multiqc.collect{ it[1]} )
.mix(LAST_SPLIT_O2O.out.multiqc.collect{ it[1]} )
m2o = LAST_LASTAL_M2O.out.maf
o2o = LAST_SPLIT_O2O.out.maf
versions = LAST_LASTDB.out.versions
}

/*
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24 changes: 17 additions & 7 deletions workflows/pairgenomealign.nf
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Expand Up @@ -53,8 +53,6 @@ workflow PAIRGENOMEALIGN {
ASSEMBLYSCAN (
ch_samplesheet
)
ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLYSCAN.out.json.collect{it[1]})
ch_versions = ch_versions.mix(ASSEMBLYSCAN.out.versions.first())

// Prefix query ids with target genome name before producing alignment files
ch_samplesheet = ch_samplesheet
Expand All @@ -72,6 +70,7 @@ workflow PAIRGENOMEALIGN {
SEQTK_CUTN_TARGET.out.bed,
ch_seqtk_cutn_query
)
pairalign_out = PAIRALIGN_M2O.out
} else {

//
Expand All @@ -83,10 +82,17 @@ workflow PAIRGENOMEALIGN {
SEQTK_CUTN_TARGET.out.bed,
ch_seqtk_cutn_query
)
pairalign_out = PAIRALIGN_M2M.out
}

// Collate and save software versions
//

ch_versions = ch_versions
.mix(SEQTK_CUTN_TARGET.out.versions)
.mix( ASSEMBLYSCAN.out.versions)
.mix( pairalign_out.versions)

softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
Expand Down Expand Up @@ -117,10 +123,12 @@ workflow PAIRGENOMEALIGN {
ch_methods_description = Channel.value(
methodsDescriptionText(ch_multiqc_custom_methods_description))

ch_multiqc_files = ch_multiqc_files.mix(
ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(
ch_multiqc_files = ch_multiqc_files
.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
.mix(ASSEMBLYSCAN.out.json.collect{it[1]})
.mix(pairalign_out.multiqc)
.mix(ch_collated_versions)
.mix(
ch_methods_description.collectFile(
name: 'methods_description_mqc.yaml',
sort: true
Expand All @@ -131,7 +139,9 @@ workflow PAIRGENOMEALIGN {
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
ch_multiqc_logo.toList(),
[],
[]
)

emit:
Expand Down