Merge pull request #244 from grst/cellranger-multiqc

Add cellranger to multiqc report
nf-core · Aug 16, 2023 · 03bf3bf · 03bf3bf
2 parents 09da46b + 8b5707b
commit 03bf3bf
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Showing 8 changed files with 37 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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

diff --git a/modules.json b/modules.json
@@ -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": {
@@ -37,7 +37,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/count": {
@@ -52,7 +52,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf
diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -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")) {
@@ -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"}
+        }
     }
 
     // Run universc pipeline
@@ -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(),