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add fastp and ngsbits to multiqc input #647

Merged
merged 13 commits into from
Nov 15, 2024
Merged

add fastp and ngsbits to multiqc input #647

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3d598b7
add file to multiqc input
peterpru Nov 11, 2024
ef2f644
add ngsbits output
peterpru Nov 11, 2024
cfc6aed
remove extra line
peterpru Nov 11, 2024
492d827
Merge branch 'dev' into add-fastp-to-multiqc
peterpru Nov 11, 2024
cc9f6a1
add modules to multiqc
peterpru Nov 11, 2024
a30ab4b
fix parenthesis
peterpru Nov 11, 2024
8a72c28
make fastp output optional
peterpru Nov 15, 2024
59a9911
make optional using if
peterpru Nov 15, 2024
85c1277
use align out
peterpru Nov 15, 2024
73e8505
add samplegender from sex_check
peterpru Nov 15, 2024
434d1c7
Merge branch 'dev' into add-fastp-to-multiqc
ramprasadn Nov 15, 2024
92004b2
add changelog
peterpru Nov 15, 2024
b8deb72
Update CHANGELOG.md
ramprasadn Nov 15, 2024
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3 changes: 3 additions & 0 deletions assets/multiqc_config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ run_modules:
- qualimap
- picard
- mosdepth
- ngsbits
- peddy
- custom_content

Expand All @@ -38,6 +39,8 @@ module_order:
name: "fastp"
- mosdepth:
name: "Mosdepth"
- ngsbits:
name: "ngsbits"
- peddy:
name: "Peddy"

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2 changes: 2 additions & 0 deletions workflows/raredisease.nf
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Expand Up @@ -902,6 +902,8 @@ workflow RAREDISEASE {
)

ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([]))
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