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Add cellranger to multiqc report #244

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merged 6 commits into from Aug 16, 2023
Merged

Add cellranger to multiqc report #244

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64cb157
Add cellranger to multiqc report
grst Jun 29, 2023
97dc965
Update CHANGELOG
grst Jun 29, 2023
3555ef8
Initialize with empty channel
grst Jun 29, 2023
66f70ab
Merge branch 'dev' into cellranger-multiqc
grst Aug 7, 2023
2771a59
Update modules
grst Aug 7, 2023
8b5707b
Fix prettier
grst Aug 7, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fixed issue with file collisions while using cellranger ([#232](https://github.com/nf-core/scrnaseq/pull/232))
- Fix issue where multiqc inputs tried to access objects that did not exist ([#239](https://github.com/nf-core/scrnaseq/pull/239))
- Removed `public_aws_ecr` profile
- Include cellranger in MultiQC report ([#244](https://github.com/nf-core/scrnaseq/pull/244))
- Nf-core template update to v2.9 ([#245](https://github.com/nf-core/scrnaseq/pull/245))
- Update cellranger and fastqc module ([#246](https://github.com/nf-core/scrnaseq/pull/246)).
The [updated cellranger module](https://github.com/nf-core/modules/pull/3537) now automatically renames input FASTQ
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10 changes: 5 additions & 5 deletions modules.json
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Expand Up @@ -7,17 +7,17 @@
"nf-core": {
"cellranger/count": {
"branch": "master",
"git_sha": "2d67954880926029c0e8dddf37b340bf7127a878",
"git_sha": "716ef3019b66772a817b417078edce2f7b337858",
"installed_by": ["modules"]
},
"cellranger/mkgtf": {
"branch": "master",
"git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
"git_sha": "716ef3019b66772a817b417078edce2f7b337858",
"installed_by": ["modules"]
},
"cellranger/mkref": {
"branch": "master",
"git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
"git_sha": "716ef3019b66772a817b417078edce2f7b337858",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
Expand All @@ -37,7 +37,7 @@
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"kallistobustools/count": {
Expand All @@ -52,7 +52,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": ["modules"]
},
"star/genomegenerate": {
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13 changes: 8 additions & 5 deletions modules/nf-core/cellranger/count/main.nf
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9 changes: 4 additions & 5 deletions modules/nf-core/cellranger/mkgtf/main.nf
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9 changes: 4 additions & 5 deletions modules/nf-core/cellranger/mkref/main.nf
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10 changes: 7 additions & 3 deletions modules/nf-core/gunzip/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/multiqc/main.nf
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5 changes: 5 additions & 0 deletions workflows/scrnaseq.nf
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Expand Up @@ -78,6 +78,7 @@ ch_transcript_fasta = params.transcript_fasta ? file(params.transcript_fasta): [
ch_txp2gene = params.txp2gene ? file(params.txp2gene) : []
ch_multiqc_alevin = Channel.empty()
ch_multiqc_star = Channel.empty()
ch_multiqc_cellranger = Channel.empty()
if (params.barcode_whitelist) {
ch_barcode_whitelist = file(params.barcode_whitelist)
} else if (params.protocol.contains("10X")) {
Expand Down Expand Up @@ -193,6 +194,9 @@ workflow SCRNASEQ {
ch_versions = ch_versions.mix(CELLRANGER_ALIGN.out.ch_versions)
ch_mtx_matrices = ch_mtx_matrices.mix(CELLRANGER_ALIGN.out.cellranger_out)
ch_star_index = CELLRANGER_ALIGN.out.star_index
ch_multiqc_cellranger = CELLRANGER_ALIGN.out.cellranger_out.map{
meta, outs -> outs.findAll{ it -> it.name == "web_summary.html"}
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Why is this part necessary? Is this something that could be changed in the CELLRANGER_ALIGN module to make it play nicely with multiqc out of the box?

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It's mostly to make MultiQC more efficient, because it only gets the files it needs (the full cellranger output dir contains a lot of files)

}
}

// Run universc pipeline
Expand Down Expand Up @@ -244,6 +248,7 @@ workflow SCRNASEQ {
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{ meta, qcfile -> qcfile }.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_alevin.collect{ meta, qcfile -> qcfile }.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{ meta, qcfile -> qcfile }.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_cellranger.collect().ifEmpty([]))

MULTIQC (
ch_multiqc_files.collect(),
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