Merge pull request #18 from lianov/dev

Various updates: Fix #17, disables umi-tools qc in MultiQC, adds missing versions and updates outputs

CITATIONS.md

@@ -48,6 +48,10 @@
 
   > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
 
+- [ToulligQC](https://github.com/GenomiqueENS/toulligQC)
+
+  >Karine Dias, Bérengère Laffay, Lionel Ferrato-Berberian, Sophie Lemoine, Ali Hamraoui, Morgane Thomas-Chollier, Stéphane Le Crom and Laurent Jourdren.
+
 - [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
 
   > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.

docs/output.md

@@ -27,10 +27,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Other steps](#other-steps)
   - [UCSC](#ucsc) - Annotation BED file
 - [Quality Control](#quality-control)
-  - [FastQC](#fastqc) - Fastq QC
-  - [Nanocomp](#nanocomp) - Long Read Fastq QC
-  - [Nanoplot](#nanoplot) - Long Read Fastq QC
-  - [ToulligQC](#toulligqc) - Long Read Fastq QC
+  - [FastQC](#fastqc) - FASTQ QC
+  - [Nanocomp](#nanocomp) - Long Read FASTQ QC
+  - [Nanoplot](#nanoplot) - Long Read FASTQ QC
+  - [ToulligQC](#toulligqc) - Long Read FASTQ QC
   - [RSeQC](#rseqc) - Various RNA-seq QC metrics
   - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@@ -165,8 +165,6 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 </details>
 
-![MultiQC - umitools dedup](images/umitools_dedup.png)
-
 [UMI-Tools](https://umi-tools.readthedocs.io/en/latest/reference/dedup.html) deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. The identification of duplicate reads is performed in an error-aware manner by building networks of related UMIs
 
 ## Feature-Barcode Quantification
@@ -222,13 +220,7 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 - `<sample_identifier>/`
   - `qc/`
     - `fastqc/`
-      - `pre_trim/`
-        - `*_fastqc.html`: FastQC report containing quality metrics.
-        - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-      - `post_trim/`
-        - `*_fastqc.html`: FastQC report containing quality metrics.
-        - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-      - `post_extract/`
+      - `pre_trim/` and `post_trim/` and `post_extract/`
         - `*_fastqc.html`: FastQC report containing quality metrics.
         - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
 
@@ -273,7 +265,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 - `<sample_identifier>/`
   - `qc/`
     - `nanoplot/`
-      - `pre_trim/` and `post_trim/` and `post_extract`
+      - `pre_trim/` and `post_trim/` and `post_extract/`
         - `NanoPlot_*.log`: This is the log file detailing the nanoplot run
         - `NanoPlot-report.html` - This is browser-viewable report that contains all the figures in a single location.
         - `*.html`: Nanoplot outputs all the figures in the report as individual files that can be inspected separately.

modules.json

@@ -43,7 +43,8 @@
                     "nanoplot": {
                         "branch": "master",
                         "git_sha": "a31407dfaf0cb0d04768d5cb439fc6f4523a6981",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/nanoplot/nanoplot.diff"
                     },
                     "rseqc/readdistribution": {
                         "branch": "master",
@@ -93,7 +94,8 @@
                     "toulligqc": {
                         "branch": "master",
                         "git_sha": "061a322293b3487e53f044304710e54cbf657717",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/toulligqc/toulligqc.diff"
                     },
                     "umitools/dedup": {
                         "branch": "master",

workflows/scnanoseq.nf

@@ -563,9 +563,11 @@ workflow SCNANOSEQ {
         //
         SEURAT_GENE ( ch_gene_count_mtx.join(ch_dedup_sorted_flagstat, by: [0]) )
         ch_gene_seurat_qc = SEURAT_GENE.out.seurat_stats
+        ch_versions = ch_versions.mix(SEURAT_GENE.out.versions)
 
         SEURAT_TRANSCRIPT ( ch_transcript_count_mtx.join(ch_dedup_sorted_flagstat, by: [0]) )
         ch_transcript_seurat_qc = SEURAT_TRANSCRIPT.out.seurat_stats
+        ch_versions = ch_versions.mix(SEURAT_TRANSCRIPT.out.versions)
 
         //
         // MODULE: Combine Seurat Stats
@@ -650,7 +652,8 @@ workflow SCNANOSEQ {
         ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_flagstat.collect{it[1]}.ifEmpty([]))
         ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_sorted_idxstats.collect{it[1]}.ifEmpty([]))
 
-        ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_log.collect{it[1]}.ifEmpty([]))
+        // see issue #12 (too many files when split by chr)
+        //ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_dedup_log.collect{it[1]}.ifEmpty([]))
 
         ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_gene_stats_combined.collect().ifEmpty([]))
         ch_multiqc_finalqc_files = ch_multiqc_finalqc_files.mix(ch_transcript_stats_combined.collect().ifEmpty([]))