FEAT: Add CheckQC

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#202](https://github.com/nf-core/seqinspector/pull/202) Added support for fasta fai file as input (via params or igenomes) for the pipeline
 - [#206](https://github.com/nf-core/seqinspector/pull/206) Added FASTQE for more comprehensive QC of FASTQ files
 - [#208](https://github.com/nf-core/seqinspector/pull/208) Add FASTQ linting for early validation with FQ/LINT
+- [#212](https://github.com/nf-core/seqinspector/pull/212) Add CheckQC module
 
 ### `Fixed`
 

CITATIONS.md

@@ -14,6 +14,10 @@
 
   > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
 
+- [checkQC](https://github.com/Molmed/checkQC)
+
+  > Åslin et al., (2018). CheckQC: Quick quality control of Illumina sequencing runs. Journal of Open Source Software, 3(22), 556, https://doi.org/10.21105/joss.00556
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

README.md

@@ -37,6 +37,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | `Trimming`          | [`Fastp`](https://github.com/OpenGene/fastp)                                                                        | Trimming of reads. Only performs trimming if `--tools` parameter is given.                    | [RNA, DNA, synthetic]   | [N/A]                                                                                   | no           |
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                   | yes          |
+| `QC`                | [`checkQC`](https://github.com/Molmed/checkQC)                                                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | no           |
 | `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                | [`FASTQE`](https://fastqe.com/)                                                                                     | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                   | yes          |
@@ -58,6 +59,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | Tool        | Version |
 | ----------- | ------- |
 | bwamem2     | 2.3     |
+| checkQC     | 4.1.0   |
 | fq/lint     | 0.12.0  |
 | fastp       | 1.1.0   |
 | fastqc      | 0.12.1  |

docs/output.md

@@ -13,6 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [FASTQE](#fastqe) - Raw read QC
+- [CheckQC](#checkqc) - QC of an Illumina run
 - [SeqFu Stats](#seqfu-stats) - Statistics for FASTA or FASTQ files
 - [FastQ Screen](#fastq-screen) - Mapping against a set of references for basic contamination QC
 - [BWA-MEM2_INDEX](#bwamem2_index) - Create BWA-MEM2 index of a chosen reference genome OR use pre-built index
@@ -48,6 +49,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### CheckQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `checkqc/`
+  - `checkqc_report.json`: Reports sequencing metrics that are not fulfilled. Note that the CheckQC module in MultiQC currently does not support BCL Convert data, so if the report if based on data from that demultiplexer it will not be visualized in the MutliQC report. Results can be found in the output directory.
+
+</details>
+
 ### FastP
 
 [FastP](https://github.com/OpenGene/fastp) is a tool designed to provide all-in-one preprocessing for FastQ files and as such is used for trimming and splitting.

docs/usage.md

@@ -168,7 +168,8 @@ It is possible to also chose bundles of pre-specified tools using the `tools_bun
 
 Currently, the following bundles are available:
 
-:::info{title="default"}{collapse}
+<details>
+<summary>default</summary>
 
 Requirements:
 
@@ -183,9 +184,10 @@ Tools:
 - rundirparser
 - seqfu_stats
 
-:::
+</details>
 
-:::info{title="all"}{collapse}
+<details>
+<summary>all</summary>
 
 Requirements:
 
@@ -194,16 +196,17 @@ Requirements:
 
 Tools:
 
+- checkQC
 - fastqc
 - fastqscreen
 - picard_collecthsmetrics
 - picard_collectmultiplemetrics
 - rundirparser
 - seqfu_stats
+</details>
 
-:::
-
-:::info{title="minimal"}{collapse}
+<details>
+<summary>minimal</summary>
 
 Requirements:
 
@@ -215,10 +218,10 @@ Tools:
 - fastqscreen
 - picard_collectmultiplemetrics
 - seqfu_stats
+</details>
 
-:::
-
-:::info{title="bam"}{collapse}
+<details>
+<summary>bam</summary>
 
 Requirements:
 
@@ -229,39 +232,41 @@ Tools:
 - picard_collecthsmetrics
 - picard_collectmultiplemetrics
 
-:::
+</details>
 
-:::info{title="fastq"}{collapse}
+<details>
+<summary>fastq</summary>
 
 Tools:
 
 - fastqc
 - fastqscreen
 
-:::
+</details>
 
-:::info{title="illumina"}{collapse}
+<details>
+<summary>illumina</summary>
 
 Requirements:
 
 - Specification of the Illumina runfolder
 
 Tools:
 
+- checkQC
 - rundirparser
 - seqfu_stats
+</details>
 
-:::
-
-:::info{title="ont"}{collapse}
+<details>
+<summary>ont</summary>
 
 Tools:
 
 - fastqc
 - fastqscreen
 - seqfu_stats
-
-:::
+</details>
 
 ### Available functionality and tools
 
@@ -367,6 +372,17 @@ A pipeline might not always support every possible argument or option of a parti
 
 To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
 
+#### Custom config for checkQC
+
+To run checkQC with custom configuration, add a yml file with the custom configuration to the rundir and add the following code block to any of your [nextflow config files](https://www.nextflow.io/docs/latest/config.html#configuration-files).
+
+```bash
+process {
+    withName: CHECKQC {
+        ext.args = '--config */custom_checkqc.yml'
+    }
+```
+
 ### nf-core/configs
 
 In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

modules.json

@@ -15,6 +15,11 @@
                         "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a",
                         "installed_by": ["modules"]
                     },
+                    "checkqc": {
+                        "branch": "master",
+                        "git_sha": "389ed64090aa4594276fb3d53923432c7728c5b4",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "1fb5a73bce8e4ac7079b0a9461b23d11e877ad14",
@@ -33,8 +38,7 @@
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
+                        "installed_by": ["modules"]
                     },
                     "fq/lint": {
                         "branch": "master",

nextflow_schema.json

@@ -51,7 +51,7 @@
                 "tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to run",
-                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|fq_lint|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-sort-amount-asc"
                 },
                 "tools_bundle": {
@@ -63,7 +63,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip - overrides any other means of tools selection",
-                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|fq_lint|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-window-close "
                 }
             }