FIX: resolve conflicts

nf-core · Nov 22, 2024 · 336af63 · 336af63
2 parents 31def65 + d6844f2
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diff --git a/CITATIONS.md b/CITATIONS.md
@@ -82,6 +82,8 @@
 
   > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.
 
+- [ToulligQC](https://github.com/GenomiqueENS/toulligQC)
+
 - [UCSC tools](https://www.ncbi.nlm.nih.gov/pubmed/20639541/)
 
   > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.

diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s
 
 1. Demultiplexing ([`qcat`](https://github.com/nanoporetech/qcat); _optional_)
 2. Raw read cleaning ([NanoLyse](https://github.com/wdecoster/nanolyse); _optional_)
-3. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+3. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`ToulligQC`](https://github.com/GenomiqueENS/toulligQC), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. Alignment ([`GraphMap2`](https://github.com/lbcb-sci/graphmap2) or [`minimap2`](https://github.com/lh3/minimap2))
    - Both aligners are capable of performing unspliced and spliced alignment. Sensible defaults will be applied automatically based on a combination of the input data and user-specified parameters
    - Each sample can be mapped to its own reference genome if multiplexed in this way

diff --git a/conf/modules.config b/conf/modules.config
@@ -94,6 +94,18 @@ if (!params.skip_qc) {
             }
         }
     }
+    if (!params.skip_toulligqc) {
+        process {
+            withName: TOULLIGQC {
+                publishDir = [
+                    path: { "${params.outdir}/toulligqc" },
+                    mode: 'copy',
+                    enabled: true,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+        }
+    }
     if (!params.skip_fastqc) {
         process {
             withName: FASTQC {

diff --git a/docs/images/toulligqc_report_barcodes.png b/docs/images/toulligqc_report_barcodes.png
diff --git a/docs/output.md b/docs/output.md
@@ -54,11 +54,14 @@ If you would like to run NanoLyse on the raw FASTQ files you can provide `--run_
 - `nanoplot/fastq/<SAMPLE>/`: directory with various `*.html` files containing QC metrics and plots.
 - `fastqc/<SAMPLE>_fastqc.html`: _FastQC_ `*.html` file for each sample.
 - `fastqc/<SAMPLE>_fastqc.zip`: _FastQC_ `*.zip` file for each sample.
+- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/report.html`: _ToulligQC_ `*.html` browser-viewable report that contains all the figures in a single location for each sample.
+- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/report.data`: A log file containing information about ToulligQC execution, environment variables and full statistics.
+- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/images/*`: This is folder containing all the individual images produced by ToulligQC.
 
 </details>
 
 _Documentation_:
-[NanoPlot](https://github.com/wdecoster/NanoPlot), [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)
+[NanoPlot](https://github.com/wdecoster/NanoPlot), [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/), [ToulligQC](https://github.com/GenomiqueENS/toulligQC)
 
 _Description_:
 _NanoPlot_ can be used to produce general quality metrics from the per barcode FASTQ files generated by a basecaller e.g. quality score distribution, read lengths, and other general stats.
@@ -67,6 +70,10 @@ _NanoPlot_ can be used to produce general quality metrics from the per barcode F
 
 _FastQC_ can give general quality metrics about your reads. It can provide information about the quality score distribution across your reads, and the per-base sequence content (%A/C/G/T). You can also generate information about adapter contamination and other over-represented sequences.
 
+_ToulligQC_ is dedicated to the QC analyses of Oxford Nanopore runs. It can be used to produce general quality metrics from the per barcode FASTQ files generated by a basecaller e.g. quality score distribution, read lengths, and other general stats. You can also generate quality metrics per barcode.
+
+![ToulligQC - Barcoding Report](images/toulligqc_barcoding_report.png)
+
 ## Alignment
 
 <details markdown="1">

diff --git a/modules.json b/modules.json
@@ -7,168 +7,129 @@
                 "nf-core": {
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "d6d112a1af2ee8c97fc1932df008183341e7d8fe",
-                        "installed_by": ["modules"]
-                    },
-                    "bedtools/bamtobed": {
-                        "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
-                        "installed_by": ["modules"]
-                    },
-                    "bedtools/genomecov": {
-                        "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": ["modules"]
-                    },
-                    "custom/getchromsizes": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "cutesv": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "deepvariant": {
-                        "branch": "master",
-                        "git_sha": "ed67f2fadd6d2a155b296f728e6b1f8c92ddc1a6",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "a33464f205fa15305bfe268546f6607b6f4d4753",
-                        "installed_by": ["modules"]
-                    },
-                    "graphmap2/align": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "graphmap2/index": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "minimap2/align": {
-                        "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
-                    },
-                    "minimap2/index": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
-                        "installed_by": ["modules"]
+                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "nanolyse": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "nanoplot": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "qcat": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "3822e04e49b6d89b7092feb3480d744cb5d9986b",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/view": {
-                        "branch": "master",
-                        "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
-                        "installed_by": ["modules"]
-                    },
-                    "sniffles": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "stringtie/merge": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "stringtie/stringtie": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "subread/featurecounts": {
-                        "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "90294980a903ecebd99ac31d8b6c66af48fa8259",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
-                    },
-                    "ucsc/bedgraphtobigwig": {
-                        "branch": "master",
-                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
-                        "installed_by": ["modules"]
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
-                    "ucsc/bedtobigbed": {
+                    "toulligqc": {
                         "branch": "master",
-                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
-                        "installed_by": ["modules"]
+                        "git_sha": "061a322293b3487e53f044304710e54cbf657717",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
-                        "installed_by": ["modules"]
+                        "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7",
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },

diff --git a/modules/nf-core/toulligqc/environment.yml b/modules/nf-core/toulligqc/environment.yml
diff --git a/modules/nf-core/toulligqc/main.nf b/modules/nf-core/toulligqc/main.nf